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Error trying to use a trained model on new data #130

Closed mbcooper97 closed 5 months ago

mbcooper97 commented 5 months ago

I am using KPMS on our supercomputing cluster (A100 GPUs & HPC Linux Desktop). I have trained a network using data from DeepLabCut and have additional videos + DLC files that I would like analyzed on this network. When I try to use the apply network function, I get an error about my files not being a valid JAX type. There seems to be a problem with how KPMS is accessing the new data. Any thoughts or suggestions?

[mbullock@c0246 ~]$ module load Anaconda3
[mbullock@c0246 ~]$ module load CUDA/11.8.0
[mbullock@c0246 ~]$ module load GCCcore/10.3.0
[mbullock@c0246 ~]$ module load cuDNN/8.9.2.26-CUDA-11.8.0
[mbullock@c0246 ~]$ conda activate keypoint_moseq
(keypoint_moseq) [mbullock@c0246 ~]$ python

Python 3.9.18 | packaged by conda-forge | (main, Aug 30 2023, 03:49:32) [GCC 12.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.

>import keypoint_moseq as kpms
> project_dir = '/home/mbullock/Desktop/Teton_3-5moKPMS/'
>config = lambda: kpms.load_config(project_dir)
>dlc_config = '/home/mbullock/Desktop/Teton_3-5mo/config.yaml'
> keypoint_data_path = '/home/mbullock/Desktop/Teton_3-5moKPMS/'
> keypoint_data_path = '/home/mbullock/Desktop/NewYoungTeton'
>coordinates, confidences, bodyparts = kpms.load_keypoints(keypoint_data_path, 'deeplabcut')

Loading keypoints: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 22/22 [00:05<00:00, 4.29it/s]

> data, metadata = kpms.format_data(coordinates, confidences, **config())
> pca = kpms.load_pca(project_dir)
> kpms.update_config(project_dir, latent_dim=4)
> model = kpms.load_checkpoint(project_dir, model_name)[0]

Traceback (most recent call last): File "", line 1, in NameError: name 'model_name' is not defined

> model_name = '2024_02_05-11_34_09'
> model = kpms.load_checkpoint(project_dir, model_name)[0]
> new_data = '/home/mbullock/Desktop/NewYoungTeton'
> coordinates, confidences, bodyparts = kpms.load_keypoints(new_data, 'deeplabcut')

Loading keypoints: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 22/22 [00:01<00:00, 12.81it/s]

> data, metadata = kpms.format_data(coordinates, confidences, **config())
> results = kpms.apply_model(model, data, metadata, project_dir, model_name, **config())

Traceback (most recent call last): File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/_src/dispatch.py", line 1296, in _device_put_impl a = xla.abstractify(x) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/interpreters/xla.py", line 273, in abstractify if aval_fn: return aval_fn(x) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/_src/abstract_arrays.py", line 36, in make_shaped_array dtype = dtypes.canonicalize_dtype(dtypes.result_type(x)) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/_src/dtypes.py", line 484, in result_type dtype, weak_type = _lattice_resulttype(*(float if arg is None else arg for arg in args)) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/_src/dtypes.py", line 452, in _lattice_result_type dtypes, weak_types = zip((_dtype_and_weaktype(arg) for arg in args)) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/_src/dtypes.py", line 452, in dtypes, weak_types = zip((_dtype_and_weaktype(arg) for arg in args)) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/_src/dtypes.py", line 300, in _dtype_and_weaktype return dtype(value), any(value is typ for typ in _weak_types) or is_weakly_typed(value) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/_src/dtypes.py", line 447, in dtype raise TypeError(f"Value '{x}' with dtype {dt} is not a valid JAX array " TypeError: Value '['3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' 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'529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000']' with dtype <U62 is not a valid JAX array type. Only arrays of numeric types are supported by JAX. The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "", line 1, in File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/keypoint_moseq/fitting.py", line 281, in apply_model data = jax.device_put(data) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/_src/api.py", line 2827, in device_put return tree_map(lambda y: dispatch.device_put_p.bind(y, device=device), x) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/_src/tree_util.py", line 200, in tree_map return treedef.unflatten(f(xs) for xs in zip(all_leaves)) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/_src/tree_util.py", line 200, in return treedef.unflatten(f(xs) for xs in zip(all_leaves)) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/_src/api.py", line 2827, in return tree_map(lambda y: dispatch.device_put_p.bind(y, device=device), x) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/core.py", line 328, in bind return self.bind_with_trace(find_top_trace(args), args, params) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/core.py", line 331, in bind_with_trace out = trace.process_primitive(self, map(trace.full_raise, args), params) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/core.py", line 698, in process_primitive return primitive.impl(*tracers, **params) File "/home/mbullock/.conda/envs/keypoint_moseq/lib/python3.9/site-packages/jax/_src/dispatch.py", line 1298, in _device_put_impl raise TypeError( TypeError: Argument '['3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3698-01032024104245DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3701-01032024104319DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3701-01032024104319DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3701-01032024104319DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3701-01032024104319DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3701-01032024104319DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3701-01032024104319DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3701-01032024104319DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3701-01032024104319DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3701-01032024104319DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3701-01032024104319DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3701-01032024104319DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3702-01032024115610DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3702-01032024115610DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3702-01032024115610DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3702-01032024115610DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3702-01032024115610DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3702-01032024115610DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3702-01032024115610DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3702-01032024115610DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3702-01032024115610DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3702-01032024115610DLC_resnet50_Teton3-5moJan25shuffle1_694000' '3702-01032024115610DLC_resnet50_Teton3-5moJan25shuffle1_694000' '507-01032024104429DLC_resnet50_Teton3-5moJan25shuffle1_694000' 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'524-01112024134810DLC_resnet50_Teton3-5moJan25shuffle1_694000' '524-01112024134810DLC_resnet50_Teton3-5moJan25shuffle1_694000' '524-01112024134810DLC_resnet50_Teton3-5moJan25shuffle1_694000' '527-01052024131932DLC_resnet50_Teton3-5moJan25shuffle1_694000' '527-01052024131932DLC_resnet50_Teton3-5moJan25shuffle1_694000' '527-01052024131932DLC_resnet50_Teton3-5moJan25shuffle1_694000' '527-01052024131932DLC_resnet50_Teton3-5moJan25shuffle1_694000' '527-01052024131932DLC_resnet50_Teton3-5moJan25shuffle1_694000' '527-01052024131932DLC_resnet50_Teton3-5moJan25shuffle1_694000' '527-01052024131932DLC_resnet50_Teton3-5moJan25shuffle1_694000' '527-01052024131932DLC_resnet50_Teton3-5moJan25shuffle1_694000' '527-01052024131932DLC_resnet50_Teton3-5moJan25shuffle1_694000' '527-01052024131932DLC_resnet50_Teton3-5moJan25shuffle1_694000' '527-01052024131932DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '529-01112024135120DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '530-01192024112016DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '531-01192024112102DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000' '532-01192024122730DLC_resnet50_Teton3-5moJan25shuffle1_694000']' of type <class 'numpy.ndarray'> is not a valid JAX type

calebweinreb commented 5 months ago

What versions do you get with

import keypoint_moseq
print(keypoint_moseq.__version__)
import jax_moseq
print(jax_moseq.__version__)

?

mbcooper97 commented 5 months ago

Thanks for the quick reply! This is what I get: >>> print(keypoint_moseq.__version__) 0.2.5

>>> import jax_moseq
>>> print(jax_moseq.__version__)

0.1.0

calebweinreb commented 5 months ago

The error is caused by a mismatch between the code in version 0.2.5 and newest version of the code. The tutorial is written for the newer version. So you have two options:

1) Update to the latest version of the code (which will unfortunately mean you have to fit a new model) 2) Keep using version 0.2.5 and use commands from the 0.2.5-era tutorial

mbcooper97 commented 5 months ago

I updated to the current version. This resolved the issue. Thanks!