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umyelab / LabGym

Quantify user-defined behaviors.
GNU General Public License v3.0
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[Train categorizer] ValueError when training categorizer - 'y has 0 samples' #75

Closed karinmcode closed 10 months ago

karinmcode commented 10 months ago

When attempting to train a categorizer clicking on the Train the Categorizer, a ValueError is raised due to an empty array of labels y.

Screenshot 2023-11-09 at 18 10 53

Thank you for your help.

Error message (short): 

Traceback (most recent call last):
...
File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/LabGym/categorizers.py", line 1017, in train_combnet
labels=lb.fit_transform(labels)
...
ValueError: y has 0 samples: array([], dtype=float64)

Error message: 

(labgym) karinmorandell@karins-mbp-2 ~ % python3 -m LabGym                                 
Traceback (most recent call last):
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/scipy/__init__.py", line 143, in <module>
    from scipy._lib._ccallback import LowLevelCallable
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/scipy/_lib/_ccallback.py", line 1, in <module>
    from . import _ccallback_c
  File "_ccallback_c.pyx", line 209, in init scipy._lib._ccallback_c
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/ctypes/__init__.py", line 8, in <module>
    from _ctypes import Union, Structure, Array
ImportError: dlopen(/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/lib-dynload/_ctypes.cpython-310-darwin.so, 0x0002): Library not loaded: @rpath/libffi.8.dylib
  Referenced from: <179FE86B-D7D3-3317-91A0-93B90E328260> /Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/lib-dynload/_ctypes.cpython-310-darwin.so
  Reason: tried: '/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/lib-dynload/../../libffi.8.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/lib-dynload/../../libffi.8.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/Users/karinmorandell/miniconda3/envs/labgym/bin/../lib/libffi.8.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/Users/karinmorandell/miniconda3/envs/labgym/bin/../lib/libffi.8.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/usr/local/lib/libffi.8.dylib' (no such file), '/usr/lib/libffi.8.dylib' (no such file, not in dyld cache)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/LabGym/__main__.py", line 1, in <module>
    from . import gui
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/LabGym/gui.py", line 26, in <module>
    from .gui_categorizers import WindowLv2_GenerateExamples,WindowLv2_TrainCategorizers,WindowLv2_TestCategorizers
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/LabGym/gui_categorizers.py", line 26, in <module>
    from .analyzebehaviors import AnalyzeAnimal
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/LabGym/analyzebehaviors.py", line 21, in <module>
    from .tools import *
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/LabGym/tools.py", line 26, in <module>
    import scipy.ndimage as ndimage
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/scipy/__init__.py", line 148, in <module>
    raise ImportError(msg) from e
ImportError: The `scipy` install you are using seems to be broken, (extension modules cannot be imported), please try reinstalling.
(labgym) karinmorandell@karins-mbp-2 ~ % conda deactivate 
(base) karinmorandell@karins-mbp-2 ~ % conda remove --name labgym --all

Remove all packages in environment /Users/karinmorandell/miniconda3/envs/labgym:

## Package Plan ##

  environment location: /Users/karinmorandell/miniconda3/envs/labgym

The following packages will be REMOVED:

  alabaster-0.7.12-pyhd3eb1b0_0
  applaunchservices-0.3.0-py310hecd8cb5_0
  appnope-0.1.2-py310hecd8cb5_1001
  arrow-1.2.3-py310hecd8cb5_1
  astroid-2.14.2-py310hecd8cb5_0
  asttokens-2.0.5-pyhd3eb1b0_0
  atomicwrites-1.4.0-py_0
  attrs-23.1.0-py310hecd8cb5_0
  autopep8-1.6.0-pyhd3eb1b0_1
  babel-2.11.0-py310hecd8cb5_0
  backcall-0.2.0-pyhd3eb1b0_0
  beautifulsoup4-4.12.2-py310hecd8cb5_0
  binaryornot-0.4.4-pyhd3eb1b0_1
  black-23.3.0-py310hecd8cb5_0
  bleach-4.1.0-pyhd3eb1b0_0
  brotli-python-1.0.9-py310he9d5cce_7
  bzip2-1.0.8-h620ffc9_4
  ca-certificates-2023.08.22-hecd8cb5_0
  certifi-2023.7.22-py310hecd8cb5_0
  cffi-1.15.1-py310h6c40b1e_3
  chardet-4.0.0-py310hecd8cb5_1003
  charset-normalizer-2.0.4-pyhd3eb1b0_0
  click-8.1.7-py310hecd8cb5_0
  cloudpickle-2.2.1-py310hecd8cb5_0
  colorama-0.4.6-py310hecd8cb5_0
  comm-0.1.2-py310hecd8cb5_0
  cookiecutter-1.7.3-pyhd3eb1b0_0
  cryptography-41.0.3-py310h30e54ef_0
  cyrus-sasl-2.1.28-h3973f50_1
  debugpy-1.6.7-py310hcec6c5f_0
  decorator-5.1.1-pyhd3eb1b0_0
  defusedxml-0.7.1-pyhd3eb1b0_0
  diff-match-patch-20200713-pyhd3eb1b0_0
  dill-0.3.7-py310hecd8cb5_0
  docstring-to-markdown-0.11-py310hecd8cb5_0
  docutils-0.18.1-py310hecd8cb5_3
  exceptiongroup-1.0.4-py310hecd8cb5_0
  executing-0.8.3-pyhd3eb1b0_0
  flake8-6.0.0-py310hecd8cb5_0
  gettext-0.21.0-he85b6c0_1
  glib-2.69.1-hfff2838_2
  gst-plugins-base-1.14.1-hcec6c5f_1
  gstreamer-1.14.1-h6c40b1e_1
  icu-73.1-hcec6c5f_0
  idna-3.4-py310hecd8cb5_0
  imagesize-1.4.1-py310hecd8cb5_0
  importlib-metadata-6.0.0-py310hecd8cb5_0
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  inflection-0.5.1-py310hecd8cb5_0
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  ipython_genutils-0.2.0-pyhd3eb1b0_1
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  jpeg-9e-h6c40b1e_1
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  jupyter_client-8.6.0-py310hecd8cb5_0
  jupyter_core-5.5.0-py310hecd8cb5_0
  jupyterlab_pygments-0.1.2-py_0
  keyring-23.13.1-py310hecd8cb5_0
  krb5-1.20.1-h428f121_1
  lazy-object-proxy-1.6.0-py310hca72f7f_0
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  libclang13-14.0.6-default_habbcc1a_1
  libcxx-14.0.6-h9765a3e_0
  libedit-3.1.20221030-h6c40b1e_0
  libffi-3.4.4-hecd8cb5_0
  libiconv-1.16-hca72f7f_2
  libllvm14-14.0.6-h91fad77_3
  libpng-1.6.39-h6c40b1e_0
  libpq-12.15-h04015c4_1
  libsodium-1.0.18-h1de35cc_0
  libspatialindex-1.9.3-h23ab428_0
  libxml2-2.10.4-h1bd7e62_1
  llvm-openmp-14.0.6-h0dcd299_0
  lz4-c-1.9.4-hcec6c5f_0
  markupsafe-2.1.1-py310hca72f7f_0
  matplotlib-inline-0.1.6-py310hecd8cb5_0
  mccabe-0.7.0-pyhd3eb1b0_0
  mistune-2.0.4-py310hecd8cb5_0
  more-itertools-8.12.0-pyhd3eb1b0_0
  mypy_extensions-1.0.0-py310hecd8cb5_0
  mysql-5.7.24-h1a8d504_2
  nbclient-0.8.0-py310hecd8cb5_0
  nbconvert-7.10.0-py310hecd8cb5_0
  nbformat-5.9.2-py310hecd8cb5_0
  ncurses-6.4-hcec6c5f_0
  nest-asyncio-1.5.6-py310hecd8cb5_0
  numpydoc-1.5.0-py310hecd8cb5_0
  openssl-3.0.12-h1a28f6b_0
  packaging-23.1-py310hecd8cb5_0
  pandocfilters-1.5.0-pyhd3eb1b0_0
  parso-0.8.3-pyhd3eb1b0_0
  pathspec-0.10.3-py310hecd8cb5_0
  pcre-8.45-h23ab428_0
  pexpect-4.8.0-pyhd3eb1b0_3
  pickleshare-0.7.5-pyhd3eb1b0_1003
  pip-23.3-py310hecd8cb5_0
  platformdirs-3.10.0-py310hecd8cb5_0
  pluggy-1.0.0-py310hecd8cb5_1
  ply-3.11-py310hecd8cb5_0
  poyo-0.5.0-pyhd3eb1b0_0
  prompt-toolkit-3.0.36-py310hecd8cb5_0
  psutil-5.9.0-py310hca72f7f_0
  ptyprocess-0.7.0-pyhd3eb1b0_2
  pure_eval-0.2.2-pyhd3eb1b0_0
  pycodestyle-2.10.0-py310hecd8cb5_0
  pycparser-2.21-pyhd3eb1b0_0
  pydocstyle-6.3.0-py310hecd8cb5_0
  pyflakes-3.0.1-py310hecd8cb5_0
  pygments-2.15.1-py310hecd8cb5_1
  pylint-2.16.2-py310hecd8cb5_0
  pylint-venv-2.3.0-py310hecd8cb5_0
  pyls-spyder-0.4.0-pyhd3eb1b0_0
  pyobjc-core-9.0-py310h9205ec4_1
  pyobjc-framework-cocoa-9.0-py310h9205ec4_0
  pyobjc-framework-coreservices-9.0-py310h46256e1_0
  pyobjc-framework-fsevents-9.0-py310hecd8cb5_0
  pyopenssl-23.2.0-py310hecd8cb5_0
  pyqt-5.15.10-py310hcec6c5f_0
  pyqt5-sip-12.13.0-py310h6c40b1e_0
  pyqtwebengine-5.15.10-py310hcec6c5f_0
  pysocks-1.7.1-py310hecd8cb5_0
  python-3.10.13-hb885b13_0
  python-dateutil-2.8.2-pyhd3eb1b0_0
  python-fastjsonschema-2.16.2-py310hecd8cb5_0
  python-lsp-black-1.2.1-py310hecd8cb5_0
  python-lsp-jsonrpc-1.0.0-pyhd3eb1b0_0
  python-lsp-server-1.7.2-py310hecd8cb5_0
  python-slugify-5.0.2-pyhd3eb1b0_0
  python.app-3-py310hca72f7f_0
  pytoolconfig-1.2.5-py310hecd8cb5_1
  pytz-2023.3.post1-py310hecd8cb5_0
  pyyaml-6.0.1-py310h6c40b1e_0
  pyzmq-25.1.0-py310hcec6c5f_0
  qdarkstyle-3.0.2-pyhd3eb1b0_0
  qstylizer-0.2.2-py310hecd8cb5_0
  qt-main-5.15.2-hf83fbd5_10
  qt-webengine-5.15.9-h90a370e_7
  qtawesome-1.2.2-py310hecd8cb5_0
  qtconsole-5.4.2-py310hecd8cb5_0
  qtpy-2.2.0-py310hecd8cb5_0
  readline-8.2-hca72f7f_0
  referencing-0.30.2-py310hecd8cb5_0
  requests-2.31.0-py310hecd8cb5_0
  rope-1.7.0-py310hecd8cb5_0
  rpds-py-0.10.6-py310hf2ad997_0
  rtree-1.0.1-py310hecd8cb5_0
  setuptools-68.0.0-py310hecd8cb5_0
  sip-6.7.12-py310hcec6c5f_0
  six-1.16.0-pyhd3eb1b0_1
  snowballstemmer-2.2.0-pyhd3eb1b0_0
  sortedcontainers-2.4.0-pyhd3eb1b0_0
  soupsieve-2.5-py310hecd8cb5_0
  sphinx-5.0.2-py310hecd8cb5_0
  sphinxcontrib-applehelp-1.0.2-pyhd3eb1b0_0
  sphinxcontrib-devhelp-1.0.2-pyhd3eb1b0_0
  sphinxcontrib-htmlhelp-2.0.0-pyhd3eb1b0_0
  sphinxcontrib-jsmath-1.0.1-pyhd3eb1b0_0
  sphinxcontrib-qthelp-1.0.3-pyhd3eb1b0_0
  sphinxcontrib-serializinghtml-1.1.5-pyhd3eb1b0_0
  spyder-5.4.3-py310hecd8cb5_1
  spyder-kernels-2.4.4-py310hecd8cb5_0
  sqlite-3.41.2-h6c40b1e_0
  stack_data-0.2.0-pyhd3eb1b0_0
  text-unidecode-1.3-pyhd3eb1b0_0
  textdistance-4.2.1-pyhd3eb1b0_0
  three-merge-0.1.1-pyhd3eb1b0_0
  tinycss2-1.2.1-py310hecd8cb5_0
  tk-8.6.12-h5d9f67b_0
  toml-0.10.2-pyhd3eb1b0_0
  tomli-2.0.1-py310hecd8cb5_0
  tomlkit-0.11.1-py310hecd8cb5_0
  tornado-6.3.3-py310h6c40b1e_0
  traitlets-5.7.1-py310hecd8cb5_0
  typing-extensions-4.7.1-py310hecd8cb5_0
  typing_extensions-4.7.1-py310hecd8cb5_0
  tzdata-2023c-h04d1e81_0
  ujson-5.4.0-py310he9d5cce_0
  unidecode-1.2.0-pyhd3eb1b0_0
  urllib3-1.26.18-py310hecd8cb5_0
  watchdog-2.1.6-py310h999c104_0
  wcwidth-0.2.5-pyhd3eb1b0_0
  webencodings-0.5.1-py310hecd8cb5_1
  whatthepatch-1.0.2-py310hecd8cb5_0
  wheel-0.41.2-py310hecd8cb5_0
  wrapt-1.14.1-py310hca72f7f_0
  wurlitzer-3.0.2-py310hecd8cb5_0
  xz-5.4.2-h80987f9_0
  yaml-0.2.5-haf1e3a3_0
  yapf-0.31.0-pyhd3eb1b0_0
  zeromq-4.3.4-h23ab428_0
  zipp-3.11.0-py310hecd8cb5_0
  zlib-1.2.13-h4dc903c_0
  zstd-1.5.5-hc035e20_0

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(base) karinmorandell@karins-mbp-2 ~ % conda create -n labgym python=3.10
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/karinmorandell/miniconda3/envs/labgym

  added / updated specs:
    - python=3.10

The following NEW packages will be INSTALLED:

  bzip2              pkgs/main/osx-arm64::bzip2-1.0.8-h620ffc9_4 
  ca-certificates    pkgs/main/osx-arm64::ca-certificates-2023.08.22-hca03da5_0 
  libffi             pkgs/main/osx-arm64::libffi-3.4.4-hca03da5_0 
  ncurses            pkgs/main/osx-arm64::ncurses-6.4-h313beb8_0 
  openssl            pkgs/main/osx-arm64::openssl-3.0.12-h1a28f6b_0 
  pip                pkgs/main/osx-arm64::pip-23.3-py310hca03da5_0 
  python             pkgs/main/osx-arm64::python-3.10.13-hb885b13_0 
  readline           pkgs/main/osx-arm64::readline-8.2-h1a28f6b_0 
  setuptools         pkgs/main/osx-arm64::setuptools-68.0.0-py310hca03da5_0 
  sqlite             pkgs/main/osx-arm64::sqlite-3.41.2-h80987f9_0 
  tk                 pkgs/main/osx-arm64::tk-8.6.12-hb8d0fd4_0 
  tzdata             pkgs/main/noarch::tzdata-2023c-h04d1e81_0 
  wheel              pkgs/main/osx-arm64::wheel-0.41.2-py310hca03da5_0 
  xz                 pkgs/main/osx-arm64::xz-5.4.2-h80987f9_0 
  zlib               pkgs/main/osx-arm64::zlib-1.2.13-h5a0b063_0 

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate labgym
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) karinmorandell@karins-mbp-2 ~ % conda activate labgym

(labgym) karinmorandell@karins-mbp-2 ~ % pip install LabGym

Collecting LabGym
  Using cached LabGym-2.2.2-py3-none-any.whl
Collecting tensorflow (from LabGym)
  Using cached tensorflow-2.14.0-cp310-cp310-macosx_12_0_arm64.whl.metadata (3.3 kB)
Collecting matplotlib (from LabGym)
  Using cached matplotlib-3.8.1-cp310-cp310-macosx_11_0_arm64.whl.metadata (5.8 kB)
Collecting opencv-contrib-python (from LabGym)
  Using cached opencv_contrib_python-4.8.1.78-cp37-abi3-macosx_11_0_arm64.whl.metadata (19 kB)
Collecting opencv-python (from LabGym)
  Using cached opencv_python-4.8.1.78-cp37-abi3-macosx_11_0_arm64.whl.metadata (19 kB)
Collecting openpyxl (from LabGym)
  Using cached openpyxl-3.1.2-py2.py3-none-any.whl (249 kB)
Collecting xlsxwriter (from LabGym)
  Using cached XlsxWriter-3.1.9-py3-none-any.whl.metadata (2.6 kB)
Collecting pandas (from LabGym)
  Using cached pandas-2.1.2-cp310-cp310-macosx_11_0_arm64.whl.metadata (18 kB)
Collecting pathlib (from LabGym)
  Using cached pathlib-1.0.1-py3-none-any.whl (14 kB)
Collecting scikit-learn (from LabGym)
  Using cached scikit_learn-1.3.2-cp310-cp310-macosx_12_0_arm64.whl.metadata (11 kB)
Collecting scikit-image (from LabGym)
  Using cached scikit_image-0.22.0-cp310-cp310-macosx_12_0_arm64.whl.metadata (13 kB)
Collecting seaborn (from LabGym)
  Using cached seaborn-0.13.0-py3-none-any.whl.metadata (5.3 kB)
Collecting wxPython (from LabGym)
  Using cached wxPython-4.2.1-cp310-cp310-macosx_10_10_universal2.whl.metadata (2.9 kB)
Collecting scikit-posthocs (from LabGym)
  Using cached scikit_posthocs-0.8.0-py3-none-any.whl.metadata (5.9 kB)
Collecting torch (from LabGym)
  Using cached torch-2.1.0-cp310-none-macosx_11_0_arm64.whl.metadata (24 kB)
Collecting torchvision (from LabGym)
  Using cached torchvision-0.16.0-cp310-cp310-macosx_11_0_arm64.whl.metadata (6.6 kB)
Collecting contourpy>=1.0.1 (from matplotlib->LabGym)
  Using cached contourpy-1.2.0-cp310-cp310-macosx_11_0_arm64.whl.metadata (5.8 kB)
Collecting cycler>=0.10 (from matplotlib->LabGym)
  Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib->LabGym)
  Using cached fonttools-4.44.0-cp310-cp310-macosx_10_9_universal2.whl.metadata (153 kB)
Collecting kiwisolver>=1.3.1 (from matplotlib->LabGym)
  Using cached kiwisolver-1.4.5-cp310-cp310-macosx_11_0_arm64.whl.metadata (6.4 kB)
Collecting numpy<2,>=1.21 (from matplotlib->LabGym)
  Using cached numpy-1.26.1-cp310-cp310-macosx_11_0_arm64.whl.metadata (61 kB)
Collecting packaging>=20.0 (from matplotlib->LabGym)
  Using cached packaging-23.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pillow>=8 (from matplotlib->LabGym)
  Using cached Pillow-10.1.0-cp310-cp310-macosx_11_0_arm64.whl.metadata (9.5 kB)
Collecting pyparsing>=2.3.1 (from matplotlib->LabGym)
  Using cached pyparsing-3.1.1-py3-none-any.whl.metadata (5.1 kB)
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Installing collected packages: pytz, pathlib, mpmath, libclang, flatbuffers, xlsxwriter, wrapt, urllib3, tzdata, typing-extensions, threadpoolctl, termcolor, tensorflow-io-gcs-filesystem, tensorflow-estimator, tensorboard-data-server, sympy, six, pyparsing, pyasn1, protobuf, pillow, packaging, oauthlib, numpy, networkx, MarkupSafe, markdown, lazy_loader, kiwisolver, keras, joblib, idna, grpcio, gast, fsspec, fonttools, filelock, et-xmlfile, cycler, charset-normalizer, certifi, cachetools, absl-py, wxPython, werkzeug, tifffile, scipy, rsa, requests, python-dateutil, pyasn1-modules, patsy, opt-einsum, openpyxl, opencv-python, opencv-contrib-python, ml-dtypes, jinja2, imageio, h5py, google-pasta, contourpy, astunparse, torch, scikit-learn, scikit-image, requests-oauthlib, pandas, matplotlib, google-auth, torchvision, statsmodels, seaborn, google-auth-oauthlib, tensorboard, scikit-posthocs, tensorflow-macos, tensorflow, LabGym
Successfully installed LabGym-2.2.2 MarkupSafe-2.1.3 absl-py-2.0.0 astunparse-1.6.3 cachetools-5.3.2 certifi-2023.7.22 charset-normalizer-3.3.2 contourpy-1.2.0 cycler-0.12.1 et-xmlfile-1.1.0 filelock-3.13.1 flatbuffers-23.5.26 fonttools-4.44.0 fsspec-2023.10.0 gast-0.5.4 google-auth-2.23.4 google-auth-oauthlib-1.0.0 google-pasta-0.2.0 grpcio-1.59.2 h5py-3.10.0 idna-3.4 imageio-2.32.0 jinja2-3.1.2 joblib-1.3.2 keras-2.14.0 kiwisolver-1.4.5 lazy_loader-0.3 libclang-16.0.6 markdown-3.5.1 matplotlib-3.8.1 ml-dtypes-0.2.0 mpmath-1.3.0 networkx-3.2.1 numpy-1.26.1 oauthlib-3.2.2 opencv-contrib-python-4.8.1.78 opencv-python-4.8.1.78 openpyxl-3.1.2 opt-einsum-3.3.0 packaging-23.2 pandas-2.1.2 pathlib-1.0.1 patsy-0.5.3 pillow-10.0.1 protobuf-4.25.0 pyasn1-0.5.0 pyasn1-modules-0.3.0 pyparsing-3.1.1 python-dateutil-2.8.2 pytz-2023.3.post1 requests-2.31.0 requests-oauthlib-1.3.1 rsa-4.9 scikit-image-0.22.0 scikit-learn-1.3.2 scikit-posthocs-0.8.0 scipy-1.11.3 seaborn-0.13.0 six-1.16.0 statsmodels-0.14.0 sympy-1.12 tensorboard-2.14.1 tensorboard-data-server-0.7.2 tensorflow-2.14.0 tensorflow-estimator-2.14.0 tensorflow-io-gcs-filesystem-0.34.0 tensorflow-macos-2.14.0 termcolor-2.3.0 threadpoolctl-3.2.0 tifffile-2023.9.26 torch-2.1.0 torchvision-0.16.0 typing-extensions-4.8.0 tzdata-2023.3 urllib3-2.0.7 werkzeug-3.0.1 wrapt-1.14.1 wxPython-4.2.1 xlsxwriter-3.1.9
(labgym) karinmorandell@karins-mbp-2 ~ % python3 -m LabGym                 
/Users/karinmorandell/miniconda3/envs/labgym/bin/python3: No module named LabGym.__main__; 'LabGym' is a package and cannot be directly executed
(labgym) karinmorandell@karins-mbp-2 ~ % python3 -m LabGym
You need to install Detectron2 to use the Detector module in LabGym:
https://detectron2.readthedocs.io/en/latest/tutorials/install.html
You need to install Detectron2 to use the Detector module in LabGym:
https://detectron2.readthedocs.io/en/latest/tutorials/install.html
The user interface initialized!
2023-11-09 17:59:36.548 python3[30092:841822] +[CATransaction synchronize] called within transaction
2023-11-09 17:59:53.448 python3[30092:841822] +[CATransaction synchronize] called within transaction
2023-11-09 18:00:03.703 python3[30092:841822] +[CATransaction synchronize] called within transaction
2023-11-09 18:00:03.895 python3[30092:841822] +[CATransaction synchronize] called within transaction
2023-11-09 18:00:03.996 python3[30092:841822] +[CATransaction synchronize] called within transaction
2023-11-09 18:00:04.374 python3[30092:841822] +[CATransaction synchronize] called within transaction
2023-11-09 18:00:04.476 python3[30092:841822] +[CATransaction synchronize] called within transaction
2023-11-09 18:00:04.579 python3[30092:841822] +[CATransaction synchronize] called within transaction
2023-11-09 18:00:04.711 python3[30092:841822] +[CATransaction synchronize] called within transaction
Behavior names are: ['running', 'walking', 'adjusting', 'grooming', 'resting']
All prepared training examples stored in: /Users/karinmorandell/Library/CloudStorage/GoogleDrive-karinmorandell.pro@gmail.com/My Drive/Research/Schneider lab/Paper/Karin paper version 230911/Reviewers requests/Fig 5 Automated behavior classification/LabGym-master/data/prepared_behavioral_examples
2023-11-09 18:03:11.523 python3[30092:841822] +[CATransaction synchronize] called within transaction
2023-11-09 18:03:16.074 python3[30092:841822] +[CATransaction synchronize] called within transaction
2023-11-09 18:03:16.176 python3[30092:841822] +[CATransaction synchronize] called within transaction
2023-11-09 18:03:16.291 python3[30092:841822] +[CATransaction synchronize] called within transaction
2023-11-09 18:04:05.586 python3[30092:841822] +[CATransaction synchronize] called within transaction
2023-11-09 18:04:11.973 python3[30092:841822] +[CATransaction synchronize] called within transaction
Training Categorizer with both Animation Analyzer and Pattern Recognizer using the behavior examples in: /Users/karinmorandell/Library/CloudStorage/GoogleDrive-karinmorandell.pro@gmail.com/My Drive/Research/Schneider lab/Paper/Karin paper version 230911/Reviewers requests/Fig 5 Automated behavior classification/LabGym-master/data/prepared_training_examples
Traceback (most recent call last):
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/LabGym/gui_categorizers.py", line 1079, in train_categorizer
    CA.train_combnet(self.data_path,self.path_to_categorizer,self.out_path,dim_tconv=self.dim_tconv,dim_conv=self.dim_conv,channel=self.channel,time_step=self.length,level_tconv=self.level_tconv,level_conv=self.level_conv,aug_methods=self.aug_methods,augvalid=self.augvalid,include_bodyparts=self.include_bodyparts,std=self.std,background_free=self.background_free,behavior_mode=self.behavior_mode,social_distance=self.social_distance)
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/LabGym/categorizers.py", line 1017, in train_combnet
    labels=lb.fit_transform(labels)
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/sklearn/preprocessing/_label.py", line 329, in fit_transform
    return self.fit(y).transform(y)
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/sklearn/base.py", line 1152, in wrapper
    return fit_method(estimator, *args, **kwargs)
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/sklearn/preprocessing/_label.py", line 303, in fit
    raise ValueError("y has 0 samples: %r" % y)
ValueError: y has 0 samples: array([], dtype=float64)
karinmcode commented 10 months ago

I copied video/images from the prepared behavioral_examples to the prepared_training_examples folder.

Now, I get a different error: 

Perform augmentation for the behavior examples...
This might take hours or days, depending on the capacity of your computer.
2023-11-09 18:14:39.227315
Start to augment training examples...
Start to augment validation examples...
[ WARN:0@1153.251] global loadsave.cpp:248 findDecoder imread_('/Users/karinmorandell/Library/CloudStorage/GoogleDrive-karinmorandell.pro@gmail.com/My Drive/Research/Schneider lab/Paper/Karin paper version 230911/Reviewers requests/Fig 5 Automated behavior classification/LabGym-master/data/prepared_training_examples/13_resting.jpg'): can't open/read file: check file path/integrity
Traceback (most recent call last):
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/LabGym/gui_categorizers.py", line 1079, in train_categorizer
    CA.train_combnet(self.data_path,self.path_to_categorizer,self.out_path,dim_tconv=self.dim_tconv,dim_conv=self.dim_conv,channel=self.channel,time_step=self.length,level_tconv=self.level_tconv,level_conv=self.level_conv,aug_methods=self.aug_methods,augvalid=self.augvalid,include_bodyparts=self.include_bodyparts,std=self.std,background_free=self.background_free,behavior_mode=self.behavior_mode,social_distance=self.social_distance)
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/LabGym/categorizers.py", line 1047, in train_combnet
    test_animations,test_pattern_images,testY=self.build_data(test_files,dim_tconv=dim_tconv,dim_conv=dim_conv,channel=channel,time_step=time_step,aug_methods=aug_methods,background_free=background_free,behavior_mode=behavior_mode)
  File "/Users/karinmorandell/miniconda3/envs/labgym/lib/python3.10/site-packages/LabGym/categorizers.py", line 379, in build_data
    pattern_image=cv2.resize(pattern_image,(dim_conv,dim_conv),interpolation=cv2.INTER_AREA)
cv2.error: OpenCV(4.8.1) /Users/xperience/GHA-OpenCV-Python/_work/opencv-python/opencv-python/opencv/modules/imgproc/src/resize.cpp:4062: error: (-215:Assertion failed) !ssize.empty() in function 'resize'
yujiahu415 commented 10 months ago

Hi,

These errors might be originated from the same cause: the path to the files was not properly read by sklearn or openCV. This might be because the google drive path contain some special characters like '@'. Have you tried to do these steps locally, or avoid including '@', '-', ' ', or '.' in your file directories?

karinmcode commented 10 months ago

Thank you very much. That solved my issue.