All of the sudden getting: ValueError('need at least one array to stack') ValueError: need at least one array to stack.

[juliagorman]

I have started labeling 320/450 frames and all of the sudden as I go to add a new Instance, I dont get a new instance and instead I get this error. It continues for all future frames that I jump to and try to add an instance for. I have not run training yet or anything

File "C:\ProgramData\Anaconda3\envs\sleap\lib\site-packages\numpy\core\shape_base.py", line 423, in stack raise ValueError('need at least one array to stack') ValueError: need at least one array to stack.

---

Steps:

1. Go to new Labeling Suggestion frame
2. Right click and select "Default" to add new instance
3. Observe error (instance is not added):

Traceback (most recent call last):
  File "d:\social-leap-estimates-animal-poses\pull-requests\sleap\sleap\gui\widgets\video.py", line 376, in <lambda>
    init_method="template", location=scene_pos
  File "d:\social-leap-estimates-animal-poses\pull-requests\sleap\sleap\gui\commands.py", line 515, in newInstance
    mark_complete=mark_complete,
  File "d:\social-leap-estimates-animal-poses\pull-requests\sleap\sleap\gui\commands.py", line 241, in execute
    command().execute(context=self, params=kwargs)
  File "d:\social-leap-estimates-animal-poses\pull-requests\sleap\sleap\gui\commands.py", line 138, in execute
    self.do_with_signal(context, params)
  File "d:\social-leap-estimates-animal-poses\pull-requests\sleap\sleap\gui\commands.py", line 162, in do_with_signal
    cls.do_action(context, params)
  File "d:\social-leap-estimates-animal-poses\pull-requests\sleap\sleap\gui\commands.py", line 2762, in do_action
    center_point=location,
  File "d:\social-leap-estimates-animal-poses\pull-requests\sleap\sleap\gui\commands.py", line 2888, in add_nodes_from_template
    skeleton=instance.skeleton
  File "d:\social-leap-estimates-animal-poses\pull-requests\sleap\sleap\io\dataset.py", line 1198, in get_template_instance_points
    template_points = align.get_template_points_array(first_n_instances)
  File "d:\social-leap-estimates-animal-poses\pull-requests\sleap\sleap\info\align.py", line 219, in get_template_points_array
    points = get_instances_points(instances)
  File "d:\social-leap-estimates-animal-poses\pull-requests\sleap\sleap\info\align.py", line 214, in get_instances_points
    return np.stack([inst.points_array for inst in instances])
  File "<__array_function__ internals>", line 6, in stack
  File "C:\Users\TalmoLab\miniconda3\envs\sleap_nix\lib\site-packages\numpy\core\shape_base.py", line 422, in stack
    raise ValueError('need at least one array to stack')
ValueError: need at least one array to stack

[roomrys]

Hi @juliagorman,

Are you able to share your .slp with [email protected]? I shouldn't need your video, just the .slp is good.

Thanks,
Liezl

[roomrys]

So it seems all the options to add a new instance that reference previous instances are resulting in the traceback above. The Force Directed and Random options still seems to work since they does not reference a previous instance. After adding an instance using one of these two methods, the Default add instance method starts working again because np.stack has at least one array to stack.

...and wouldn't you know - it's another error caused by having multiple skeletons in the project.

@juliagorman Which version are you on and did you use the Load Skeleton button and/or merge your project at any point?

Thanks,
Liezl

[juliagorman]

Hi, sorry just saw this. I accidentally loaded the wrong skeleton and then added a second one. I thought I deleted the first but I guess I didn't! Thank you for your help :)

[roomrys]

Hi @juliagorman,

Thanks for the reply! Do you recall using the Load Skeleton button and which version of SLEAP are you on? Hoping that this is resolved in the newer versions (as expected, but sometimes the unexpected seems to happen).

Thanks,
Liezl