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talmolab / sleap

A deep learning framework for multi-animal pose tracking.
https://sleap.ai
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KeyError on maDLC import #1649

Open dprotter opened 8 months ago

dprotter commented 8 months ago

Bug description

Unable to load maDLC training data into SLEAP due to key error, similar to #676 and #702

Expected behaviour

Expected to import using File -> import -> DeepLabCut Dataset, and selecting either the .yaml file or a training data CSV file. This is a dataset that has been moved from another computer, which may have an effect.

Actual behaviour

Import fails with a KeyError

Your personal set up

Environment packages absl-py==1.0.0 astunparse==1.6.3 attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1640799537051/work backports.zoneinfo==0.2.1 cached-property @ file:///home/conda/feedstock_root/build_artifacts/cached_property_1615209429212/work cachetools==4.2.4 cattrs @ file:///home/conda/feedstock_root/build_artifacts/cattrs_1604136207372/work certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1700303426725/work/certifi charset-normalizer==2.0.9 cloudpickle @ file:///home/conda/feedstock_root/build_artifacts/cloudpickle_1674202310934/work cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1635519461629/work cytoolz @ file:///home/conda/feedstock_root/build_artifacts/cytoolz_1657553457169/work dask @ file:///home/conda/feedstock_root/build_artifacts/dask-core_1644602974678/work efficientnet==1.0.0 flatbuffers==2.0 fonttools @ file:///home/conda/feedstock_root/build_artifacts/fonttools_1666389892786/work fsspec @ file:///home/conda/feedstock_root/build_artifacts/fsspec_1674184942191/work gast==0.4.0 google-auth==2.3.3 google-auth-oauthlib==0.4.6 google-pasta==0.2.0 grpcio==1.43.0 h5py @ file:///home/conda/feedstock_root/build_artifacts/h5py_1604753641401/work hdmf==3.6.1 idna==3.3 image-classifiers==1.0.0 imagecodecs @ file:///home/conda/feedstock_root/build_artifacts/imagecodecs_1644819473370/work imageio @ file:///home/conda/feedstock_root/build_artifacts/imageio_1702571712725/work imgaug @ file:///home/conda/feedstock_root/build_artifacts/imgaug_1640909786103/work imgstore==0.2.9 importlib-metadata==4.10.0 importlib-resources==5.12.0 joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1691577114857/work jsmin @ file:///home/conda/feedstock_root/build_artifacts/jsmin_1642532731678/work jsonpickle==1.2 jsonschema==4.17.3 keras==2.7.0 Keras-Applications==1.0.8 Keras-Preprocessing==1.1.2 kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/kiwisolver_1657953088445/work libclang==12.0.0 locket @ file:///home/conda/feedstock_root/build_artifacts/locket_1650660393415/work Markdown==3.3.6 markdown-it-py @ file:///home/conda/feedstock_root/build_artifacts/markdown-it-py_1677100944732/work matplotlib @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1661439848456/work mdurl @ file:///home/conda/feedstock_root/build_artifacts/mdurl_1704317613764/work munkres==1.1.4 ndx-pose==0.1.1 networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1646092782768/work nixio==1.5.3 numpy==1.19.5 oauthlib==3.1.1 opencv-python-headless==4.2.0.34 opt-einsum==3.3.0 packaging==21.3 pandas==1.3.5 partd @ file:///home/conda/feedstock_root/build_artifacts/partd_1695667515973/work patsy @ file:///home/conda/feedstock_root/build_artifacts/patsy_1703606105319/work Pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1660385854171/work pkgutil_resolve_name==1.3.10 protobuf==3.16.0 psutil @ file:///home/conda/feedstock_root/build_artifacts/psutil_1666155398032/work pyasn1==0.4.8 pyasn1-modules==0.2.8 Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1700607939962/work pykalman==0.9.5 pynwb==2.3.3 pyparsing==3.0.6 pyrsistent==0.19.3 PySide2==5.13.2 python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work python-rapidjson @ file:///home/conda/feedstock_root/build_artifacts/python-rapidjson_1665999896718/work pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1693930252784/work PyWavelets @ file:///home/conda/feedstock_root/build_artifacts/pywavelets_1649616401885/work PyYAML @ file:///home/conda/feedstock_root/build_artifacts/pyyaml_1648757092905/work pyzmq @ file:///home/conda/feedstock_root/build_artifacts/pyzmq_1663830492333/work qimage2ndarray==1.10.0 QtPy @ file:///home/conda/feedstock_root/build_artifacts/qtpy_1698112029416/work requests==2.26.0 requests-oauthlib==1.3.0 rich @ file:///home/conda/feedstock_root/build_artifacts/rich-split_1700160075651/work/dist rsa==4.8 ruamel.yaml==0.17.32 ruamel.yaml.clib==0.2.7 scikit-image @ file:///home/conda/feedstock_root/build_artifacts/scikit-image_1645196656256/work scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1632611341839/work scikit-video==1.1.11 scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy_1637806658031/work seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1672497695270/work segmentation-models==1.0.1 setuptools-scm==6.3.2 Shapely @ file:///home/conda/feedstock_root/build_artifacts/shapely_1665624546039/work shiboken2==5.13.2 six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work sleap==1.3.3 statsmodels @ file:///home/conda/feedstock_root/build_artifacts/statsmodels_1654787101575/work tensorboard==2.7.0 tensorboard-data-server==0.6.1 tensorboard-plugin-wit==1.8.0 tensorflow==2.7.0 tensorflow-estimator==2.7.0 tensorflow-hub @ file:///home/conda/feedstock_root/build_artifacts/tensorflow-hub_1678880940235/work/wheel_dir/tensorflow_hub-0.13.0-py2.py3-none-any.whl tensorflow-io-gcs-filesystem==0.23.1 termcolor==1.1.0 threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1643647933166/work tifffile @ file:///home/conda/feedstock_root/build_artifacts/tifffile_1635944860688/work tomli==2.0.0 toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1657485559105/work typing_extensions==4.0.1 tzlocal==5.0.1 unicodedata2 @ file:///home/conda/feedstock_root/build_artifacts/unicodedata2_1649111917568/work urllib3==1.26.7 Werkzeug==2.0.2 wrapt==1.13.3 zipp==3.15.0 ``` # paste output of `pip freeze` or `conda list` here ```
Logs ``` $ sleap-label Saving config: /home/dprotter/.sleap/1.3.3/preferences.yaml Restoring GUI state... 2024-01-04 16:13:11.458294: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:939] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero 2024-01-04 16:13:11.465848: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:939] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero 2024-01-04 16:13:11.466161: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:939] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero Software versions: SLEAP: 1.3.3 TensorFlow: 2.7.0 Numpy: 1.19.5 Python: 3.7.12 OS: Linux-5.15.0-78-generic-x86_64-with-debian-bullseye-sid Happy SLEAPing! :) Empty filename passed to function Traceback (most recent call last): File "/home/dprotter/anaconda3/envs/sleap/lib/python3.7/site-packages/sleap/gui/commands.py", line 309, in importDLC self.execute(ImportDeepLabCut) File "/home/dprotter/anaconda3/envs/sleap/lib/python3.7/site-packages/sleap/gui/commands.py", line 242, in execute command().execute(context=self, params=kwargs) File "/home/dprotter/anaconda3/envs/sleap/lib/python3.7/site-packages/sleap/gui/commands.py", line 138, in execute self.do_with_signal(context, params) File "/home/dprotter/anaconda3/envs/sleap/lib/python3.7/site-packages/sleap/gui/commands.py", line 162, in do_with_signal cls.do_action(context, params) File "/home/dprotter/anaconda3/envs/sleap/lib/python3.7/site-packages/sleap/gui/commands.py", line 940, in do_action labels = Labels.load_deeplabcut(filename=params["filename"]) File "/home/dprotter/anaconda3/envs/sleap/lib/python3.7/site-packages/sleap/io/dataset.py", line 2192, in load_deeplabcut return read(filename, for_object="labels", as_format="deeplabcut") File "/home/dprotter/anaconda3/envs/sleap/lib/python3.7/site-packages/sleap/io/format/main.py", line 103, in read return disp.read(filename, *args, **kwargs) File "/home/dprotter/anaconda3/envs/sleap/lib/python3.7/site-packages/sleap/io/format/dispatch.py", line 57, in read return adaptor.read(file, *args, **kwargs) File "/home/dprotter/anaconda3/envs/sleap/lib/python3.7/site-packages/sleap/io/format/deeplabcut.py", line 78, in read file=file, full_video=full_video, *args, **kwargs File "/home/dprotter/anaconda3/envs/sleap/lib/python3.7/site-packages/sleap/io/format/deeplabcut.py", line 186, in read_frames data[(animal_name, node, "x")][i], File "/home/dprotter/anaconda3/envs/sleap/lib/python3.7/site-packages/pandas/core/frame.py", line 3457, in __getitem__ return self._getitem_multilevel(key) File "/home/dprotter/anaconda3/envs/sleap/lib/python3.7/site-packages/pandas/core/frame.py", line 3508, in _getitem_multilevel loc = self.columns.get_loc(key) File "/home/dprotter/anaconda3/envs/sleap/lib/python3.7/site-packages/pandas/core/indexes/multi.py", line 2932, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 725, in pandas._libs.index.BaseMultiIndexCodesEngine.get_loc File "pandas/_libs/index.pyx", line 76, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1832, in pandas._libs.hashtable.UInt64HashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1841, in pandas._libs.hashtable.UInt64HashTable.get_item KeyError: 716 ```

Screenshots

How to reproduce

  1. Move maDLC project folder to local machine
  2. Open SLEAP with $sleap-label
  3. Scroll to File -> import -> DeepLabCut Dataset
  4. Select .yaml file, or .csv file for training data (both gave the same keyerror, "716")
dprotter commented 7 months ago

I have made some progress on this front. We are using an "identity = True" project here, where 1 animal has a couple of identifying marks. These are labeled only on a single animal, so one section of the incoming datastructure has the animal label "single". Those values get added as nodes, but arent present in any other animal, so they return as a key error.

The two solutions I have had are

  1. Simply deleting those columns
  2. duplicating those columns, assigning them to the animal in which they correspond for that training data, and then duplicating the header for the other animals in the dataset but leaving the actual positional data blank.

That seems to have solved the issue. However, I will say I was using the wrong CSV file, and instead using the one locate in .../training_datasets/iteration.../.../

I think it would be helpful to add the correct target location to the documentation ( .../labeled-data/... ), as there are a few CSV files in a DLC project.