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talmolab / sleap

A deep learning framework for multi-animal pose tracking.
https://sleap.ai
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Export Labels Package not finishing #839

Closed eberrigan closed 1 year ago

eberrigan commented 2 years ago

Bug description

I would like to export the labels packages (labeled + suggested or labeled + predicted + suggested would be fine). However it stops at a certain percent (43%) and the package is never fully exported.

Expected behaviour

Package of labels, predictions and videos exported to .pkg.slp file.

Actual behaviour

It never fully exports.

Your personal set up

SLEAP: 1.2.4 TensorFlow: 2.6.3 Numpy: 1.19.5 Python: 3.7.12 OS: Windows-10-10.0.19041-SP0

Environment packages ``` (sleap_1.2.4) λ conda list # packages in environment at C:\Users\Elizabeth\.conda\envs\sleap_1.2.4: # # Name Version Build Channel absl-py 0.15.0 pypi_0 pypi anyio 3.6.1 pypi_0 pypi argon2-cffi 21.3.0 pypi_0 pypi argon2-cffi-bindings 21.2.0 pypi_0 pypi astunparse 1.6.3 pypi_0 pypi attrs 21.2.0 pypi_0 pypi babel 2.10.3 pypi_0 pypi backcall 0.2.0 pypi_0 pypi backports-zoneinfo 0.2.1 pypi_0 pypi beautifulsoup4 4.11.1 pypi_0 pypi bleach 5.0.1 pypi_0 pypi ca-certificates 2022.6.15 h5b45459_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 4.2.4 pypi_0 pypi cattrs 1.1.1 pypi_0 pypi certifi 2021.10.8 pypi_0 pypi cffi 1.15.1 pypi_0 pypi charset-normalizer 2.0.12 pypi_0 pypi clang 5.0 pypi_0 pypi colorama 0.4.5 pypi_0 pypi commonmark 0.9.1 pypi_0 pypi cuda-nvcc 11.3.58 hb8d16a4_0 nvidia cudatoolkit 11.3.1 h280eb24_10 conda-forge cudnn 8.2.1.32 h754d62a_0 conda-forge cycler 0.11.0 pypi_0 pypi debugpy 1.6.2 pypi_0 pypi decorator 5.1.1 pypi_0 pypi defusedxml 0.7.1 pypi_0 pypi efficientnet 1.0.0 pypi_0 pypi entrypoints 0.4 pypi_0 pypi fastjsonschema 2.15.3 pypi_0 pypi ffmpeg 4.3.1 ha925a31_0 conda-forge flatbuffers 1.12 pypi_0 pypi fonttools 4.33.3 pypi_0 pypi freetype 2.10.4 h546665d_1 conda-forge gast 0.4.0 pypi_0 pypi geos 3.9.1 h39d44d4_2 conda-forge google-auth 1.35.0 pypi_0 pypi google-auth-oauthlib 0.4.6 pypi_0 pypi google-pasta 0.2.0 pypi_0 pypi grpcio 1.44.0 pypi_0 pypi h5py 3.1.0 nompi_py37h19fda09_100 conda-forge hdf5 1.10.6 nompi_he0bbb20_101 conda-forge idna 3.3 pypi_0 pypi image-classifiers 1.0.0 pypi_0 pypi imageio 2.15.0 pypi_0 pypi imgaug 0.4.0 pypi_0 pypi imgstore 0.2.9 pypi_0 pypi importlib-metadata 4.11.1 pypi_0 pypi importlib-resources 5.8.0 pypi_0 pypi intel-openmp 2022.1.0 h57928b3_3787 conda-forge ipykernel 6.15.1 pypi_0 pypi ipython 7.34.0 pypi_0 pypi ipython-genutils 0.2.0 pypi_0 pypi jedi 0.18.1 pypi_0 pypi jinja2 3.1.2 pypi_0 pypi joblib 1.1.0 pypi_0 pypi jpeg 9e h8ffe710_2 conda-forge jsmin 3.0.1 pypi_0 pypi json5 0.9.8 pypi_0 pypi jsonpickle 1.2 pypi_0 pypi jsonschema 4.7.2 pypi_0 pypi jupyter-client 7.3.4 pypi_0 pypi jupyter-core 4.11.1 pypi_0 pypi jupyter-server 1.18.1 pypi_0 pypi jupyterlab 3.4.3 pypi_0 pypi jupyterlab-pygments 0.2.2 pypi_0 pypi jupyterlab-server 2.15.0 pypi_0 pypi keras 2.6.0 pypi_0 pypi keras-applications 1.0.8 pypi_0 pypi keras-preprocessing 1.1.2 pypi_0 pypi kiwisolver 1.4.3 pypi_0 pypi lcms2 2.12 h2a16943_0 conda-forge lerc 3.0 h0e60522_0 conda-forge libblas 3.9.0 15_win64_mkl conda-forge libcblas 3.9.0 15_win64_mkl conda-forge libdeflate 1.10 h8ffe710_0 conda-forge liblapack 3.9.0 15_win64_mkl conda-forge libpng 1.6.37 h1d00b33_3 conda-forge libtiff 4.3.0 hc4061b1_4 conda-forge libzlib 1.2.12 h8ffe710_1 conda-forge lz4-c 1.9.3 h8ffe710_1 conda-forge m2w64-gcc-libgfortran 5.3.0 6 conda-forge m2w64-gcc-libs 5.3.0 7 conda-forge m2w64-gcc-libs-core 5.3.0 7 conda-forge m2w64-gmp 6.1.0 2 conda-forge m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge markdown 3.3.6 pypi_0 pypi markupsafe 2.1.1 pypi_0 pypi matplotlib 3.5.2 pypi_0 pypi matplotlib-inline 0.1.3 pypi_0 pypi mistune 0.8.4 pypi_0 pypi mkl 2022.1.0 h6a75c08_874 conda-forge msys2-conda-epoch 20160418 1 conda-forge nbclassic 0.4.3 pypi_0 pypi nbclient 0.6.6 pypi_0 pypi nbconvert 6.5.0 pypi_0 pypi nbformat 5.4.0 pypi_0 pypi nest-asyncio 1.5.5 pypi_0 pypi networkx 2.6.3 pypi_0 pypi notebook-shim 0.1.0 pypi_0 pypi numpy 1.19.5 py37h4c2b6ed_3 conda-forge oauthlib 3.2.0 pypi_0 pypi olefile 0.46 pyh9f0ad1d_1 conda-forge opencv-python 4.5.5.62 pypi_0 pypi opencv-python-headless 4.5.5.62 pypi_0 pypi openjpeg 2.4.0 hb211442_1 conda-forge openssl 3.0.5 h8ffe710_0 conda-forge opt-einsum 3.3.0 pypi_0 pypi packaging 21.3 pypi_0 pypi pandas 1.3.5 py37h9386db6_0 conda-forge pandocfilters 1.5.0 pypi_0 pypi parso 0.8.3 pypi_0 pypi pickleshare 0.7.5 pypi_0 pypi pillow 8.4.0 py37hd7d9ad0_0 conda-forge pip 22.0.3 pyhd8ed1ab_0 conda-forge prometheus-client 0.14.1 pypi_0 pypi prompt-toolkit 3.0.30 pypi_0 pypi protobuf 3.19.4 pypi_0 pypi psutil 5.9.1 pypi_0 pypi pyasn1 0.4.8 pypi_0 pypi pyasn1-modules 0.2.8 pypi_0 pypi pycparser 2.21 pypi_0 pypi pygments 2.12.0 pypi_0 pypi pykalman 0.9.5 pypi_0 pypi pyparsing 3.0.7 pypi_0 pypi pyreadline 2.1 py37h03978a9_1006 conda-forge pyrsistent 0.18.1 pypi_0 pypi pyside2 5.14.1 pypi_0 pypi python 3.7.12 h900ac77_100_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-rapidjson 1.6 pypi_0 pypi python_abi 3.7 2_cp37m conda-forge pytz 2022.1 pyhd8ed1ab_0 conda-forge pytz-deprecation-shim 0.1.0.post0 pypi_0 pypi pywavelets 1.3.0 pypi_0 pypi pywin32 304 pypi_0 pypi pywinpty 2.0.6 pypi_0 pypi pyzmq 23.2.0 pypi_0 pypi qimage2ndarray 1.8.3 pypi_0 pypi requests 2.27.1 pypi_0 pypi requests-oauthlib 1.3.1 pypi_0 pypi rich 10.16.1 pypi_0 pypi scikit-image 0.19.3 pypi_0 pypi scikit-learn 1.0.2 pypi_0 pypi scikit-video 1.1.11 pypi_0 pypi scipy 1.7.3 py37hb6553fb_0 conda-forge seaborn 0.11.2 pypi_0 pypi segmentation-models 1.0.1 pypi_0 pypi send2trash 1.8.0 pypi_0 pypi setuptools 59.8.0 py37h03978a9_1 conda-forge setuptools-scm 6.4.2 pypi_0 pypi shapely 1.7.1 py37hc520ffa_5 conda-forge shiboken2 5.14.1 pypi_0 pypi six 1.15.0 pyh9f0ad1d_0 conda-forge sleap 1.2.4 pypi_0 pypi sniffio 1.2.0 pypi_0 pypi soupsieve 2.3.2.post1 pypi_0 pypi sqlite 3.39.0 h8ffe710_0 conda-forge tbb 2021.5.0 h2d74725_1 conda-forge tensorboard 2.6.0 pypi_0 pypi tensorboard-data-server 0.6.1 pypi_0 pypi tensorboard-plugin-wit 1.8.1 pypi_0 pypi tensorflow 2.6.3 pypi_0 pypi tensorflow-estimator 2.6.0 pypi_0 pypi termcolor 1.1.0 pypi_0 pypi terminado 0.15.0 pypi_0 pypi threadpoolctl 3.1.0 pypi_0 pypi tifffile 2021.11.2 pypi_0 pypi tinycss2 1.1.1 pypi_0 pypi tk 8.6.12 h8ffe710_0 conda-forge tomli 2.0.1 pypi_0 pypi tornado 6.2 pypi_0 pypi traitlets 5.3.0 pypi_0 pypi typing-extensions 3.10.0.2 pypi_0 pypi tzdata 2022.1 pypi_0 pypi tzlocal 4.2 pypi_0 pypi ucrt 10.0.20348.0 h57928b3_0 conda-forge urllib3 1.26.8 pypi_0 pypi vc 14.2 hb210afc_6 conda-forge vs2015_runtime 14.29.30037 h902a5da_6 conda-forge wcwidth 0.2.5 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi websocket-client 1.3.3 pypi_0 pypi werkzeug 2.0.3 pypi_0 pypi wheel 0.37.1 pyhd8ed1ab_0 conda-forge wrapt 1.12.1 pypi_0 pypi xz 5.2.5 h62dcd97_1 conda-forge zipp 3.7.0 pypi_0 pypi zlib 1.2.12 h8ffe710_1 conda-forge zstd 1.5.2 h6255e5f_2 conda-forge ```
Traceback ``` Traceback (most recent call last): File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\h5py\_hl\files.py", line 202, in make_fid fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl) File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py\h5f.pyx", line 96, in h5py.h5f.open OSError: Unable to open file (unable to open file: name = 'C:\Users\Elizabeth\Desktop\Phenotyping\Soy_GDM\wave_1\6-7-8domerge\metahuman\labels_678do_bad_examples.pkg.slp', errno = 13, error message = 'Permission denied', flags = 1, o_flags = 2) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\sleap\gui\commands.py", line 315, in exportFullPackage self.execute(ExportFullPackage) File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\sleap\gui\commands.py", line 237, in execute command().execute(context=self, params=kwargs) File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\sleap\gui\commands.py", line 134, in execute self.do_with_signal(context, params) File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\sleap\gui\commands.py", line 158, in do_with_signal cls.do_action(context, params) File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\sleap\gui\commands.py", line 1222, in do_action suggested=cls.suggested, File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\sleap\gui\commands.py", line 1199, in export_dataset_gui progress_callback=update_progress, File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\sleap\io\dataset.py", line 1970, in save_file write(filename, labels, *args, **kwargs) File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\sleap\io\format\main.py", line 160, in write return disp.write(filename, source_object, *args, **kwargs) File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\sleap\io\format\dispatch.py", line 78, in write return adaptor.write(filename, source_object, *args, **kwargs) File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\sleap\io\format\hdf5.py", line 253, in write progress_callback=progress_callback, File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\sleap\io\dataset.py", line 2224, in save_frame_data_hdf5 frame_numbers=frame_nums, File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\sleap\io\video.py", line 1419, in to_hdf5 with h5.File(path, "a") as f: File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\h5py\_hl\files.py", line 427, in __init__ swmr=swmr) File "C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\h5py\_hl\files.py", line 204, in make_fid fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl) File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py\h5f.pyx", line 116, in h5py.h5f.create OSError: Unable to create file (unable to open file: name = 'C:\Users\Elizabeth\Desktop\Phenotyping\Soy_GDM\wave_1\6-7-8domerge\metahuman\labels_678do_bad_examples.pkg.slp', errno = 17, error message = 'File exists', flags = 15, o_flags = 502) Saving config: C:\Users\Elizabeth/.sleap/1.2.4/preferences.yaml ```
System information ``` ==========SYSTEM========== utc: 2022-07-15 15:21:33.201909 python: 3.7.12 system: Windows, AMD64, 10, 10.0.19041 path: C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\PySide2;C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\cv2\../../x64/vc14/bin;C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\pywin32_system32;C:\Users\Elizabeth\.conda\envs\sleap_1.2.4;C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\Library\mingw-w64\bin;C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\Library\usr\bin;C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\Library\bin;C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\Scripts;C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\bin;C:\ProgramData\Miniconda3\condabin;C:\Apps\cmder\vendor\bin;C:\Apps\cmder\vendor\git-for-windows\cmd;C:\Apps\cmder\vendor\conemu-maximus5\ConEmu\Scripts;C:\Apps\cmder\vendor\conemu-maximus5;C:\Apps\cmder\vendor\conemu-maximus5\ConEmu;C:\ProgramData\Miniconda3;C:\ProgramData\Miniconda3\Library\mingw-w64\bin;C:\ProgramData\Miniconda3\Library\usr\bin;C:\ProgramData\Miniconda3\Library\bin;C:\ProgramData\Miniconda3\Scripts;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0;C:\Windows\System32\OpenSSH;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files\NVIDIA Corporation\NVIDIA NvDLISR;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;C:\WINDOWS\System32\OpenSSH;C:\Users\Elizabeth\AppData\Local\Microsoft\WindowsApps;C:\Users\Elizabeth\AppData\Local\Box\Box Edit;C:\Apps\cmder\vendor\git-for-windows\mingw64\bin;C:\Apps\cmder\vendor\git-for-windows\usr\bin;C:\Apps\cmder;C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\scipy\.libs ==========IMPORTS========== sleap import: True sleap path: C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\sleap\__init__.py sleap version: 1.2.4 pyside2 import: True pyside path: C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\PySide2\__init__.py call to C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\python.exe failed C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\python.exe: can't open file 'C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\Scripts\sleap-diagnostic': [Errno 2] No such file or directory cv2 import: True ==========GIT========== call to git failed fatal: not a git repository (or any of the parent directories): .git call to git failed fatal: not a git repository (or any of the parent directories): .git ==========TENSORFLOW========== tensorflow import: True tensorflow version: 2.6.3 tensorflow path: C:\Users\Elizabeth\.conda\envs\sleap_1.2.4\lib\site-packages\tensorflow\__init__.py gpus: [PhysicalDevice(name='/physical_device:GPU:0', device_type='GPU')] ==========CONDA========== # packages in environment at C:\Users\Elizabeth\.conda\envs\sleap_1.2.4: # # Name Version Build Channel absl-py 0.15.0 pypi_0 pypi anyio 3.6.1 pypi_0 pypi argon2-cffi 21.3.0 pypi_0 pypi argon2-cffi-bindings 21.2.0 pypi_0 pypi astunparse 1.6.3 pypi_0 pypi attrs 21.2.0 pypi_0 pypi babel 2.10.3 pypi_0 pypi backcall 0.2.0 pypi_0 pypi backports-zoneinfo 0.2.1 pypi_0 pypi beautifulsoup4 4.11.1 pypi_0 pypi bleach 5.0.1 pypi_0 pypi ca-certificates 2022.6.15 h5b45459_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 4.2.4 pypi_0 pypi cattrs 1.1.1 pypi_0 pypi certifi 2021.10.8 pypi_0 pypi cffi 1.15.1 pypi_0 pypi charset-normalizer 2.0.12 pypi_0 pypi clang 5.0 pypi_0 pypi colorama 0.4.5 pypi_0 pypi commonmark 0.9.1 pypi_0 pypi cuda-nvcc 11.3.58 hb8d16a4_0 nvidia cudatoolkit 11.3.1 h280eb24_10 conda-forge cudnn 8.2.1.32 h754d62a_0 conda-forge cycler 0.11.0 pypi_0 pypi debugpy 1.6.2 pypi_0 pypi decorator 5.1.1 pypi_0 pypi defusedxml 0.7.1 pypi_0 pypi efficientnet 1.0.0 pypi_0 pypi entrypoints 0.4 pypi_0 pypi fastjsonschema 2.15.3 pypi_0 pypi ffmpeg 4.3.1 ha925a31_0 conda-forge flatbuffers 1.12 pypi_0 pypi fonttools 4.33.3 pypi_0 pypi freetype 2.10.4 h546665d_1 conda-forge gast 0.4.0 pypi_0 pypi geos 3.9.1 h39d44d4_2 conda-forge google-auth 1.35.0 pypi_0 pypi google-auth-oauthlib 0.4.6 pypi_0 pypi google-pasta 0.2.0 pypi_0 pypi grpcio 1.44.0 pypi_0 pypi h5py 3.1.0 nompi_py37h19fda09_100 conda-forge hdf5 1.10.6 nompi_he0bbb20_101 conda-forge idna 3.3 pypi_0 pypi image-classifiers 1.0.0 pypi_0 pypi imageio 2.15.0 pypi_0 pypi imgaug 0.4.0 pypi_0 pypi imgstore 0.2.9 pypi_0 pypi importlib-metadata 4.11.1 pypi_0 pypi importlib-resources 5.8.0 pypi_0 pypi intel-openmp 2022.1.0 h57928b3_3787 conda-forge ipykernel 6.15.1 pypi_0 pypi ipython 7.34.0 pypi_0 pypi ipython-genutils 0.2.0 pypi_0 pypi jedi 0.18.1 pypi_0 pypi jinja2 3.1.2 pypi_0 pypi joblib 1.1.0 pypi_0 pypi jpeg 9e h8ffe710_2 conda-forge jsmin 3.0.1 pypi_0 pypi json5 0.9.8 pypi_0 pypi jsonpickle 1.2 pypi_0 pypi jsonschema 4.7.2 pypi_0 pypi jupyter-client 7.3.4 pypi_0 pypi jupyter-core 4.11.1 pypi_0 pypi jupyter-server 1.18.1 pypi_0 pypi jupyterlab 3.4.3 pypi_0 pypi jupyterlab-pygments 0.2.2 pypi_0 pypi jupyterlab-server 2.15.0 pypi_0 pypi keras 2.6.0 pypi_0 pypi keras-applications 1.0.8 pypi_0 pypi keras-preprocessing 1.1.2 pypi_0 pypi kiwisolver 1.4.3 pypi_0 pypi lcms2 2.12 h2a16943_0 conda-forge lerc 3.0 h0e60522_0 conda-forge libblas 3.9.0 15_win64_mkl conda-forge libcblas 3.9.0 15_win64_mkl conda-forge libdeflate 1.10 h8ffe710_0 conda-forge liblapack 3.9.0 15_win64_mkl conda-forge libpng 1.6.37 h1d00b33_3 conda-forge libtiff 4.3.0 hc4061b1_4 conda-forge libzlib 1.2.12 h8ffe710_1 conda-forge lz4-c 1.9.3 h8ffe710_1 conda-forge m2w64-gcc-libgfortran 5.3.0 6 conda-forge m2w64-gcc-libs 5.3.0 7 conda-forge m2w64-gcc-libs-core 5.3.0 7 conda-forge m2w64-gmp 6.1.0 2 conda-forge m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge markdown 3.3.6 pypi_0 pypi markupsafe 2.1.1 pypi_0 pypi matplotlib 3.5.2 pypi_0 pypi matplotlib-inline 0.1.3 pypi_0 pypi mistune 0.8.4 pypi_0 pypi mkl 2022.1.0 h6a75c08_874 conda-forge msys2-conda-epoch 20160418 1 conda-forge nbclassic 0.4.3 pypi_0 pypi nbclient 0.6.6 pypi_0 pypi nbconvert 6.5.0 pypi_0 pypi nbformat 5.4.0 pypi_0 pypi nest-asyncio 1.5.5 pypi_0 pypi networkx 2.6.3 pypi_0 pypi notebook-shim 0.1.0 pypi_0 pypi numpy 1.19.5 py37h4c2b6ed_3 conda-forge oauthlib 3.2.0 pypi_0 pypi olefile 0.46 pyh9f0ad1d_1 conda-forge opencv-python 4.5.5.62 pypi_0 pypi opencv-python-headless 4.5.5.62 pypi_0 pypi openjpeg 2.4.0 hb211442_1 conda-forge openssl 3.0.5 h8ffe710_0 conda-forge opt-einsum 3.3.0 pypi_0 pypi packaging 21.3 pypi_0 pypi pandas 1.3.5 py37h9386db6_0 conda-forge pandocfilters 1.5.0 pypi_0 pypi parso 0.8.3 pypi_0 pypi pickleshare 0.7.5 pypi_0 pypi pillow 8.4.0 py37hd7d9ad0_0 conda-forge pip 22.0.3 pyhd8ed1ab_0 conda-forge prometheus-client 0.14.1 pypi_0 pypi prompt-toolkit 3.0.30 pypi_0 pypi protobuf 3.19.4 pypi_0 pypi psutil 5.9.1 pypi_0 pypi pyasn1 0.4.8 pypi_0 pypi pyasn1-modules 0.2.8 pypi_0 pypi pycparser 2.21 pypi_0 pypi pygments 2.12.0 pypi_0 pypi pykalman 0.9.5 pypi_0 pypi pyparsing 3.0.7 pypi_0 pypi pyreadline 2.1 py37h03978a9_1006 conda-forge pyrsistent 0.18.1 pypi_0 pypi pyside2 5.14.1 pypi_0 pypi python 3.7.12 h900ac77_100_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-rapidjson 1.6 pypi_0 pypi python_abi 3.7 2_cp37m conda-forge pytz 2022.1 pyhd8ed1ab_0 conda-forge pytz-deprecation-shim 0.1.0.post0 pypi_0 pypi pywavelets 1.3.0 pypi_0 pypi pywin32 304 pypi_0 pypi pywinpty 2.0.6 pypi_0 pypi pyzmq 23.2.0 pypi_0 pypi qimage2ndarray 1.8.3 pypi_0 pypi requests 2.27.1 pypi_0 pypi requests-oauthlib 1.3.1 pypi_0 pypi rich 10.16.1 pypi_0 pypi scikit-image 0.19.3 pypi_0 pypi scikit-learn 1.0.2 pypi_0 pypi scikit-video 1.1.11 pypi_0 pypi scipy 1.7.3 py37hb6553fb_0 conda-forge seaborn 0.11.2 pypi_0 pypi segmentation-models 1.0.1 pypi_0 pypi send2trash 1.8.0 pypi_0 pypi setuptools 59.8.0 py37h03978a9_1 conda-forge setuptools-scm 6.3.2 pypi_0 pypi shapely 1.7.1 py37hc520ffa_5 conda-forge shiboken2 5.14.1 pypi_0 pypi six 1.15.0 pyh9f0ad1d_0 conda-forge sleap 1.2.4 pypi_0 pypi sniffio 1.2.0 pypi_0 pypi soupsieve 2.3.2.post1 pypi_0 pypi sqlite 3.39.0 h8ffe710_0 conda-forge tbb 2021.5.0 h2d74725_1 conda-forge tensorboard 2.6.0 pypi_0 pypi tensorboard-data-server 0.6.1 pypi_0 pypi tensorboard-plugin-wit 1.8.1 pypi_0 pypi tensorflow 2.6.3 pypi_0 pypi tensorflow-estimator 2.6.0 pypi_0 pypi termcolor 1.1.0 pypi_0 pypi terminado 0.15.0 pypi_0 pypi threadpoolctl 3.1.0 pypi_0 pypi tifffile 2021.11.2 pypi_0 pypi tinycss2 1.1.1 pypi_0 pypi tk 8.6.12 h8ffe710_0 conda-forge tomli 2.0.1 pypi_0 pypi tornado 6.2 pypi_0 pypi traitlets 5.3.0 pypi_0 pypi typing-extensions 3.10.0.2 pypi_0 pypi tzdata 2022.1 pypi_0 pypi tzlocal 4.2 pypi_0 pypi ucrt 10.0.20348.0 h57928b3_0 conda-forge urllib3 1.26.8 pypi_0 pypi vc 14.2 hb210afc_6 conda-forge vs2015_runtime 14.29.30037 h902a5da_6 conda-forge wcwidth 0.2.5 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi websocket-client 1.3.3 pypi_0 pypi werkzeug 2.0.3 pypi_0 pypi wheel 0.37.1 pyhd8ed1ab_0 conda-forge wrapt 1.12.1 pypi_0 pypi xz 5.2.5 h62dcd97_1 conda-forge zipp 3.7.0 pypi_0 pypi zlib 1.2.12 h8ffe710_1 conda-forge zstd 1.5.2 h6255e5f_2 conda-forge ==========PIP========== absl-py==0.15.0 anyio==3.6.1 argon2-cffi==21.3.0 argon2-cffi-bindings==21.2.0 astunparse==1.6.3 attrs==21.2.0 Babel==2.10.3 backcall==0.2.0 backports.zoneinfo==0.2.1 beautifulsoup4==4.11.1 bleach==5.0.1 cached-property @ file:///home/conda/feedstock_root/build_artifacts/cached_property_1615209429212/work cachetools==4.2.4 cattrs==1.1.1 certifi==2021.10.8 cffi==1.15.1 charset-normalizer==2.0.12 clang==5.0 colorama==0.4.5 commonmark==0.9.1 cycler==0.11.0 debugpy==1.6.2 decorator==5.1.1 defusedxml==0.7.1 efficientnet==1.0.0 entrypoints==0.4 fastjsonschema==2.15.3 flatbuffers==1.12 fonttools==4.33.3 gast==0.4.0 google-auth==1.35.0 google-auth-oauthlib==0.4.6 google-pasta==0.2.0 grpcio==1.44.0 h5py @ file:///D:/bld/h5py_1604753757907/work idna==3.3 image-classifiers==1.0.0 imageio==2.15.0 imgaug==0.4.0 imgstore==0.2.9 importlib-metadata==4.11.1 importlib-resources==5.8.0 ipykernel==6.15.1 ipython==7.34.0 ipython-genutils==0.2.0 jedi==0.18.1 Jinja2==3.1.2 joblib==1.1.0 jsmin==3.0.1 json5==0.9.8 jsonpickle==1.2 jsonschema==4.7.2 jupyter-client==7.3.4 jupyter-core==4.11.1 jupyter-server==1.18.1 jupyterlab==3.4.3 jupyterlab-pygments==0.2.2 jupyterlab-server==2.15.0 keras==2.6.0 Keras-Applications==1.0.8 Keras-Preprocessing==1.1.2 kiwisolver==1.4.3 Markdown==3.3.6 MarkupSafe==2.1.1 matplotlib==3.5.2 matplotlib-inline==0.1.3 mistune==0.8.4 nbclassic==0.4.3 nbclient==0.6.6 nbconvert==6.5.0 nbformat==5.4.0 nest-asyncio==1.5.5 networkx==2.6.3 notebook-shim==0.1.0 numpy @ file:///D:/bld/numpy_1649281563521/work oauthlib==3.2.0 olefile @ file:///home/conda/feedstock_root/build_artifacts/olefile_1602866521163/work opencv-python @ git+https://github.com/talmolab/wrap_opencv-python-headless.git@ede49f6a23a73033216339f29515e59d594ba921 opencv-python-headless==4.5.5.62 opt-einsum==3.3.0 packaging==21.3 pandas @ file:///D:/bld/pandas_1639398349358/work pandocfilters==1.5.0 parso==0.8.3 pickleshare==0.7.5 Pillow @ file:///D:/bld/pillow_1636559064986/work prometheus-client==0.14.1 prompt-toolkit==3.0.30 protobuf==3.19.4 psutil==5.9.1 pyasn1==0.4.8 pyasn1-modules==0.2.8 pycparser==2.21 Pygments==2.12.0 pykalman==0.9.5 pyparsing==3.0.7 pyreadline @ file:///D:/bld/pyreadline_1655703530615/work pyrsistent==0.18.1 PySide2==5.14.1 python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work python-rapidjson==1.6 pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1647961439546/work pytz-deprecation-shim==0.1.0.post0 PyWavelets==1.3.0 pywin32==304 pywinpty==2.0.6 PyYAML==6.0 pyzmq==23.2.0 qimage2ndarray==1.8.3 requests==2.27.1 requests-oauthlib==1.3.1 rich==10.16.1 rsa==4.8 scikit-image==0.19.3 scikit-learn==1.0.2 scikit-video==1.1.11 scipy @ file:///C:/bld/scipy_1637806996411/work seaborn==0.11.2 segmentation-models==1.0.1 Send2Trash==1.8.0 setuptools-scm==6.4.2 Shapely==1.7.1 shiboken2==5.14.1 six @ file:///home/conda/feedstock_root/build_artifacts/six_1590081179328/work sleap==1.2.4 sniffio==1.2.0 soupsieve==2.3.2.post1 tensorboard==2.6.0 tensorboard-data-server==0.6.1 tensorboard-plugin-wit==1.8.1 tensorflow==2.6.3 tensorflow-estimator==2.6.0 termcolor==1.1.0 terminado==0.15.0 threadpoolctl==3.1.0 tifffile==2021.11.2 tinycss2==1.1.1 tomli==2.0.1 tornado==6.2 traitlets==5.3.0 typing-extensions==3.10.0.2 tzdata==2022.1 tzlocal==4.2 urllib3==1.26.8 wcwidth==0.2.5 webencodings==0.5.1 websocket-client==1.3.3 Werkzeug==2.0.3 wrapt==1.12.1 zipp==3.7.0 ==========NVIDIA========== unable to locate nvidia-smi ```

Screenshots

bug

How to reproduce

  1. Go to Predict
  2. Click on Export Labels Package
  3. Scroll down to Labeled + Suggested or Labeled +Predicted
  4. See error
roomrys commented 1 year ago

Hi @eberrigan,

I know there was some undocumented work on this, so I am not sure - is this still a problem?

Thanks, Liezl

eberrigan commented 1 year ago

Hi @roomrys I am still having this problem. Please see my command line below. Apparently, there is something wrong with my h5 files, and I can not see them listed in the videos window. Do you think the two problems are related?

I am working locally. Thanks!

(sleap_v1.3.3) C:\Users\pbiobgh>sleap-label
Saving config: C:\Users\pbiobgh/.sleap/1.3.3/preferences.yaml
Restoring GUI state...

Software versions:
SLEAP: 1.3.3
TensorFlow: 2.7.0
Numpy: 1.21.6
Python: 3.7.12
OS: Windows-10-10.0.22621-SP0

Happy SLEAPing! :)
Traceback (most recent call last):
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 289, in openProject
    self.execute(OpenProject, filename=filename, first_open=first_open)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 242, in execute
    command().execute(context=self, params=kwargs)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 138, in execute
    self.do_with_signal(context, params)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 162, in do_with_signal
    cls.do_action(context, params)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 727, in do_action
    context.loadProjectFile(filename)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 274, in loadProjectFile
    self.execute(LoadProjectFile, filename=filename)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 242, in execute
    command().execute(context=self, params=kwargs)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 138, in execute
    self.do_with_signal(context, params)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 162, in do_with_signal
    cls.do_action(context, params)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 675, in do_action
    context.app.on_data_update([UpdateTopic.project, UpdateTopic.all])
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\app.py", line 1166, in on_data_update
    self.videos_dock.table.model().items = self.labels.videos
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\dataviews.py", line 103, in items
    item_data = self.item_to_data(obj, item)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\dataviews.py", line 392, in item_to_data
    return {key: getattr(item, key) for key in self.properties}
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\dataviews.py", line 392, in <dictcomp>
    return {key: getattr(item, key) for key in self.properties}
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\video.py", line 1046, in __getattr__
    return getattr(self.backend, item)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\video.py", line 251, in frames
    return self.__dataset_h5.shape[0]
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\video.py", line 154, in __dataset_h5
    self._load()
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\video.py", line 126, in _load
    if self.dataset + "/video" in self.__file_h5:
  File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\h5py\_hl\group.py", line 439, in __contains__
    return self._e(name) in self.id
  File "h5py\h5g.pyx", line 462, in h5py.h5g.GroupID.__contains__
  File "h5py\h5g.pyx", line 463, in h5py.h5g.GroupID.__contains__
  File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py\h5g.pyx", line 547, in h5py.h5g._path_valid
  File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py\h5o.pyx", line 168, in h5py.h5o.get_info
RuntimeError: Can't get deprecated info for object (wrong B-tree signature)
Traceback (most recent call last):
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 353, in exportTrainingPackage
    self.execute(ExportTrainingPackage)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 242, in execute
    command().execute(context=self, params=kwargs)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 138, in execute
    self.do_with_signal(context, params)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 162, in do_with_signal
    cls.do_action(context, params)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 1457, in do_action
    verbose=params.get("verbose", True),
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\gui\commands.py", line 1432, in export_dataset_gui
    progress_callback=update_progress if verbose else None,
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\dataset.py", line 1997, in save_file
    write(filename, labels, *args, **kwargs)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\format\main.py", line 162, in write
    return disp.write(filename, source_object, *args, **kwargs)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\format\dispatch.py", line 79, in write
    return adaptor.write(filename, source_object, *args, **kwargs)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\format\hdf5.py", line 253, in write
    progress_callback=progress_callback,
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\dataset.py", line 2373, in save_frame_data_hdf5
    frame_numbers=frame_nums,
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\video.py", line 1433, in to_hdf5
    frame_data = self.get_frames(frame_numbers)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\video.py", line 1117, in get_frames
    return np.stack([self.get_frame(idx) for idx in idxs], axis=0)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\video.py", line 1117, in <listcomp>
    return np.stack([self.get_frame(idx) for idx in idxs], axis=0)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\video.py", line 1104, in get_frame
    return self.backend.get_frame(idx)
  File "C:\Users\pbiobgh\.conda\envs\sleap_v1.3.3\lib\site-packages\sleap\io\video.py", line 321, in get_frame
    frame = self.__dataset_h5[idx]
TypeError: 'NoneType' object is not subscriptable
eberrigan commented 1 year ago

Fixed it! It is my h5 files :)