Integration of `sleap` with `sleap-anipose` and `anipose` #1973

martinesparza · 2024-09-26T18:01:57Z

martinesparza
Sep 26, 2024

Hi all! In my lab we are running 3d pose estimation in Anipose from 2d prediction computed in Sleap. Currently we have 3 separate environments, one for sleap, another for sleap-anipose, and a third for anipose. Is there a way of using all three in a single environment? I keep trying to install them in the same environment but get several issues. I just want to know if this is even possible

Thanks so much!!!

Martín.

Answered by martinesparza

Oct 2, 2024

Hi @roomrys,

Thanks for the thorough answer. It was really helpful in helping me identify where the conflicts are, mainly related to opencv. I have done something slightly different to get it working which goes something like this:

# Create the environment called bnp and install sleap
$ conda create -y -n myenv -c conda-forge -c nvidia -c sleap -c anaconda sleap
$ conda activate myenv 

# Remove opencv pypi version because it conflicts with sleap-anipose
$ pip uninstall -y opencv-python-headless 

# Install required version
$ pip install "opencv-contrib-python<4.7.0" 

# Install sleap anipose and anipose version 1.0
$ pip install sleap_anipose
$ pip install "anipose<1.1"

Like this, every…

View full answer

2024-09-26T18:02:11Z

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0 replies

roomrys · 2024-10-01T22:55:09Z

roomrys
Oct 1, 2024
Maintainer

Hi @martinesparza,

If you are working on the multi-view branch (liezl/add-gui-elements-for-sessions), then you should have an environment installed via this file which already includes sleap, sleap-anipose, and aniposelib (the backend for anipose).

Now, we just need to install anipose and see if things are working. At first I received an opencv error, which is due to multiple packages pulling in different flavors of opencv, but I just pip uninstalled one of the opencv's (opencv-contrib-python-4.10.0.84) that was not pulled in by anipose (opencv-python-4.6.0), and things seem to be working with my minimal sleap-label and anipose tests.

MV GUI environment.yml installation

I used this environment.yml to run the following command:

mamba env create -f environment.yml -n saa0

The terminal history cut-off a bit....

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Downloading and Extracting Packages

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\ "By downloading and using the cuDNN conda packages, you accept the terms and conditions of the NVIDIA cuDNN EULA - https://docs.nvidia.com/deeplearning/cudnn/sla/index.html" 

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Obtaining file:///D:/social-leap-estimates-animal-poses/source/sleap
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Using cached Deprecated-1.2.14-py2.py3-none-any.whl (9.6 kB)
Downloading imageio_ffmpeg-0.5.1-py3-none-win_amd64.whl (22.6 MB)
   ---------------------------------------- 22.6/22.6 MB 131.1 MB/s eta 0:00:00
Using cached imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Using cached iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
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Using cached sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB)
Using cached sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
Using cached sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Using cached sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
Using cached tzlocal-5.1-py3-none-any.whl (21 kB)
Using cached uc_micro_py-1.0.3-py3-none-any.whl (6.2 kB)
Using cached anyio-3.7.1-py3-none-any.whl (80 kB)
Using cached attrs-21.4.0-py2.py3-none-any.whl (60 kB)
Using cached bleach-6.0.0-py3-none-any.whl (162 kB)
Using cached cffi-1.15.1-cp37-cp37m-win_amd64.whl (179 kB)
Downloading cryptography-43.0.1-cp37-abi3-win_amd64.whl (3.1 MB)
   ---------------------------------------- 3.1/3.1 MB 98.6 MB/s eta 0:00:00
Using cached distlib-0.3.8-py2.py3-none-any.whl (468 kB)
Using cached entrypoints-0.4-py3-none-any.whl (5.3 kB)
Using cached filelock-3.12.2-py3-none-any.whl (10 kB)
Using cached importlib_resources-5.12.0-py3-none-any.whl (36 kB)
Downloading MarkupSafe-2.1.5-cp37-cp37m-win_amd64.whl (17 kB)
Using cached mistune-0.8.4-py2.py3-none-any.whl (16 kB)
Using cached nbclient-0.5.13-py3-none-any.whl (70 kB)
Using cached notebook-6.5.7-py3-none-any.whl (529 kB)
Using cached notebook_shim-0.2.4-py3-none-any.whl (13 kB)
Using cached pandocfilters-1.5.1-py2.py3-none-any.whl (8.7 kB)
Using cached pkgutil_resolve_name-1.3.10-py3-none-any.whl (4.7 kB)
Using cached platformdirs-4.0.0-py3-none-any.whl (17 kB)
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Using cached pyrsistent-0.19.3-cp37-cp37m-win_amd64.whl (62 kB)
Using cached pywin32-306-cp37-cp37m-win_amd64.whl (9.3 MB)
Using cached pywin32_ctypes-0.2.3-py3-none-any.whl (30 kB)
Using cached pywinpty-1.1.6-cp37-none-win_amd64.whl (1.4 MB)
Downloading ruamel.yaml-0.18.6-py3-none-any.whl (117 kB)
   ---------------------------------------- 117.8/117.8 kB ? eta 0:00:00
Using cached Send2Trash-1.8.3-py3-none-any.whl (18 kB)
Downloading SQLAlchemy-1.4.54-cp37-cp37m-win_amd64.whl (1.6 MB)
   ---------------------------------------- 1.6/1.6 MB 99.0 MB/s eta 0:00:00
Using cached terminado-0.17.1-py3-none-any.whl (17 kB)
Using cached accessible_pygments-0.0.4-py2.py3-none-any.whl (29 kB)
Using cached argon2_cffi-23.1.0-py3-none-any.whl (15 kB)
Using cached backports.zoneinfo-0.2.1-cp37-cp37m-win_amd64.whl (38 kB)
Using cached beautifulsoup4-4.12.3-py3-none-any.whl (147 kB)
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Using cached lxml-5.3.0-cp37-cp37m-win_amd64.whl (3.8 MB)
Downloading nbdime-4.0.2-py3-none-any.whl (5.9 MB)
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Downloading numba-0.56.4-cp37-cp37m-win_amd64.whl (2.5 MB)
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Using cached prometheus_client-0.17.1-py3-none-any.whl (60 kB)
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Using cached wcwidth-0.2.13-py2.py3-none-any.whl (34 kB)
Using cached websocket_client-1.6.1-py3-none-any.whl (56 kB)
Using cached GitPython-3.1.43-py3-none-any.whl (207 kB)
Downloading greenlet-3.1.1-cp37-cp37m-win_amd64.whl (298 kB)
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Using cached jupyter_server_mathjax-0.2.6-py3-none-any.whl (3.1 MB)
Downloading llvmlite-0.39.1-cp37-cp37m-win_amd64.whl (23.2 MB)
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Using cached ruamel.yaml.clib-0.2.8-cp37-cp37m-win_amd64.whl (117 kB)
Using cached sniffio-1.3.1-py3-none-any.whl (10 kB)
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Using cached argon2_cffi_bindings-21.2.0-cp36-abi3-win_amd64.whl (30 kB)
Using cached more_itertools-9.1.0-py3-none-any.whl (54 kB)
Using cached pycparser-2.21-py2.py3-none-any.whl (118 kB)
Using cached gitdb-4.0.11-py3-none-any.whl (62 kB)
Using cached smmap-5.0.1-py3-none-any.whl (24 kB)
Installing collected packages: webencodings, wcwidth, snowballstemmer, pywin32, pyvirtualdisplay, pickleshare, mistune, json5, ipython-genutils, distlib, backcall, appdirs, websocket-client, uc-micro-py, tzdata, typing-extensions, typed-ast, traitlets, tornado, toml, tinycss2, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, sniffio, smmap, Send2Trash, ruamel.yaml.clib, rfc3986, regex, qimage2ndarray, pywinpty, pywin32-ctypes, pyrsistent, pycparser, prompt-toolkit, prometheus-client, pkgutil-resolve-name, pkginfo, pathspec, parso, pandocfilters, opencv-contrib-python, nodeenv, nest-asyncio, mypy-extensions, more-itertools, MarkupSafe, lxml, llvmlite, jupyterlab-widgets, jupyterlab-pygments, iniconfig, importlib-resources, imagesize, imageio-ffmpeg, identify, greenlet, filelock, exceptiongroup, entrypoints, docutils, Deprecated, defusedxml, decorator, debugpy, coverage, colorama, cfgv, bleach, backports.zoneinfo, babel, attrs, alabaster, accessible-pygments, tzlocal, tqdm, terminado, ruamel.yaml, requests-toolbelt, readme-renderer, pyjwt, platformdirs, nixio, matplotlib-inline, markdown-it-py, livereload, linkify-it-py, keras-applications, jupyter-core, jinja2, jedi, jaraco.classes, importlib-metadata, gitdb, comm, cffi, beautifulsoup4, anyio, virtualenv, sqlalchemy, sphinx, pynacl, pluggy, numba, mdit-py-plugins, keyring, jupyter-client, jsonschema, ipython, imgstore, image-classifiers, gitpython, efficientnet, cryptography, click, argon2-cffi-bindings, twine, sphinx-togglebutton, sphinx-copybutton, sphinx-autobuild, segmentation-models, pytest, pydata-sphinx-theme, pre-commit, nbformat, myst-parser, ipykernel, hdmf, black, argon2-cffi, aniposelib, sphinx-book-theme, sleap-anipose, pytest-xvfb, pytest-qt, pytest-cov, pynwb, PyGithub, nbclient, ndx-pose, nbconvert, sleap, jupyter-server, notebook-shim, jupyterlab-server, jupyter-server-mathjax, nbdime, nbclassic, notebook, jupyterlab, jupyter-cache, widgetsnbextension, ipywidgets, jupyter-sphinx, myst-nb
  Attempting uninstall: typing-extensions
    Found existing installation: typing_extensions 4.0.1
    Uninstalling typing_extensions-4.0.1:
      Successfully uninstalled typing_extensions-4.0.1
  Attempting uninstall: attrs
    Found existing installation: attrs 24.2.0
    Uninstalling attrs-24.2.0:
      Successfully uninstalled attrs-24.2.0
  Attempting uninstall: markdown-it-py
    Found existing installation: markdown-it-py 2.2.0
    Uninstalling markdown-it-py-2.2.0:
      Successfully uninstalled markdown-it-py-2.2.0
  Attempting uninstall: importlib-metadata
    Found existing installation: importlib-metadata 4.10.0
    Uninstalling importlib-metadata-4.10.0:
      Successfully uninstalled importlib-metadata-4.10.0
  Running setup.py develop for sleap
Successfully installed Deprecated-1.2.14 MarkupSafe-2.1.5 PyGithub-2.3.0 Send2Trash-1.8.3 accessible-pygments-0.0.4 alabaster-0.7.13 aniposelib-0.5.1 anyio-3.7.1 appdirs-1.4.4 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 attrs-21.4.0 babel-2.14.0 backcall-0.2.0 backports.zoneinfo-0.2.1 beautifulsoup4-4.12.3 black-21.6b0 bleach-6.0.0 cffi-1.15.1 cfgv-3.3.1 click-8.0.4 colorama-0.4.6 comm-0.1.4 coverage-7.2.7 cryptography-43.0.1 debugpy-1.7.0 decorator-5.1.1 defusedxml-0.7.1 distlib-0.3.8 docutils-0.17.1 efficientnet-1.0.0 entrypoints-0.4 exceptiongroup-1.2.2 filelock-3.12.2 
gitdb-4.0.11 gitpython-3.1.43 greenlet-3.1.1 hdmf-3.5.5 identify-2.5.24 image-classifiers-1.0.0 imageio-ffmpeg-0.5.1 imagesize-1.4.1 imgstore-0.2.9 importlib-metadata-6.7.0 importlib-resources-5.12.0 iniconfig-2.0.0 ipykernel-6.16.2 ipython-7.34.0 ipython-genutils-0.2.0 ipywidgets-7.8.4 jaraco.classes-3.2.3 jedi-0.17.2 jinja2-3.1.4 json5-0.9.16 jsonschema-4.17.3 jupyter-cache-0.4.3 jupyter-client-7.4.9 jupyter-core-4.12.0 jupyter-server-1.13.5 jupyter-server-mathjax-0.2.6 jupyter-sphinx-0.3.2 jupyterlab-3.3.4 jupyterlab-pygments-0.2.2 jupyterlab-server-2.16.3 jupyterlab-widgets-1.1.10 keras-applications-1.0.8 keyring-24.1.1 linkify-it-py-2.0.3 livereload-2.7.0 llvmlite-0.39.1 lxml-5.3.0 markdown-it-py-1.1.0 matplotlib-inline-0.1.6 mdit-py-plugins-0.2.8 mistune-0.8.4 more-itertools-9.1.0 mypy-extensions-1.0.0 myst-nb-0.13.2 myst-parser-0.15.2 nbclassic-0.5.6 nbclient-0.5.13 nbconvert-6.5.4 nbdime-4.0.2 nbformat-5.1.3 ndx-pose-0.1.1 nest-asyncio-1.6.0 nixio-1.5.3 nodeenv-1.9.1 notebook-6.5.7 notebook-shim-0.2.4 numba-0.56.4 opencv-contrib-python-4.6.0.66 pandocfilters-1.5.1 parso-0.7.1 pathspec-0.11.2 pickleshare-0.7.5 pkginfo-1.10.0 pkgutil-resolve-name-1.3.10 platformdirs-4.0.0 pluggy-1.2.0 pre-commit-2.21.0 prometheus-client-0.17.1 prompt-toolkit-3.0.48 pycparser-2.21 pydata-sphinx-theme-0.13.3 pyjwt-2.8.0 pynacl-1.5.0 pynwb-2.3.3 pyrsistent-0.19.3 pytest-7.4.4 pytest-cov-3.0.0 pytest-qt-4.2.0 pytest-xvfb-3.0.0 pyvirtualdisplay-3.0 pywin32-306 pywin32-ctypes-0.2.3 pywinpty-1.1.6 qimage2ndarray-1.10.0 readme-renderer-37.3 regex-2024.4.16 requests-toolbelt-1.0.0 rfc3986-2.0.0 ruamel.yaml-0.18.6 ruamel.yaml.clib-0.2.8 segmentation-models-1.0.1 sleap-1.3.3 sleap-anipose-0.1.8 smmap-5.0.1 sniffio-1.3.1 snowballstemmer-2.2.0 soupsieve-2.4.1 sphinx-4.5.0 sphinx-autobuild-2021.3.14 sphinx-book-theme-1.0.1 sphinx-copybutton-0.5.2 sphinx-togglebutton-0.3.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 sqlalchemy-1.4.54 terminado-0.17.1 tinycss2-1.2.1 toml-0.10.2 tornado-6.2 tqdm-4.66.5 traitlets-5.9.0 twine-3.3.0 typed-ast-1.5.5 typing-extensions-4.7.1 tzdata-2024.2 tzlocal-5.1 uc-micro-py-1.0.3 virtualenv-20.26.6 wcwidth-0.2.13 webencodings-0.5.1 websocket-client-1.6.1 widgetsnbextension-3.6.9

done
#
# To activate this environment, use
#
#     $ conda activate saa0
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Then

mamba activate saa0

before proceeding.

anipose installation

(saa0) λ pip install anipose
Collecting anipose
  Downloading anipose-1.1.13-py3-none-any.whl.metadata (2.5 kB)
Collecting aniposelib>=0.7.0 (from anipose)
  Using cached aniposelib-0.7.0-py3-none-any.whl.metadata (1.2 kB)
Requirement already satisfied: opencv-contrib-python in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from anipose) (4.6.0.66)
Requirement already satisfied: toml in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from anipose) (0.10.2)
Requirement already satisfied: numpy in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from anipose) (1.19.5)
Requirement already satisfied: scipy in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from anipose) (1.7.3)
Requirement already satisfied: pandas in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from anipose) (1.3.5)
Requirement already satisfied: tqdm in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from anipose) (4.66.5)
Requirement already satisfied: click in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from anipose) (8.0.4)
Requirement already satisfied: scikit-video in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from anipose) (1.1.11)
Collecting flask (from anipose)
  Downloading Flask-2.2.5-py3-none-any.whl.metadata (3.9 kB)
Collecting flask-compress (from anipose)
  Downloading Flask_Compress-1.15-py3-none-any.whl.metadata (8.4 kB)
Collecting flask-ipban (from anipose)
  Downloading flask_ipban-1.1.5-py2.py3-none-any.whl.metadata (12 kB)
Collecting opencv-contrib-python (from anipose)
  Downloading opencv_contrib_python-4.10.0.84-cp37-abi3-win_amd64.whl.metadata (20 kB)
Requirement already satisfied: numba in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from aniposelib>=0.7.0->anipose) (0.56.4)
Requirement already satisfied: colorama in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from click->anipose) (0.4.6)
Requirement already satisfied: importlib-metadata in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from click->anipose) (6.7.0)
Collecting Werkzeug>=2.2.2 (from flask->anipose)
  Downloading Werkzeug-2.2.3-py3-none-any.whl.metadata (4.4 kB)
Requirement already satisfied: Jinja2>=3.0 in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from flask->anipose) (3.1.4)
Collecting itsdangerous>=2.0 (from flask->anipose)
  Downloading itsdangerous-2.1.2-py3-none-any.whl.metadata (2.9 kB)
Collecting brotli (from flask-compress->anipose)
  Downloading Brotli-1.1.0-cp37-cp37m-win_amd64.whl.metadata (5.6 kB)
Collecting zstandard (from flask-compress->anipose)
  Downloading zstandard-0.21.0-cp37-cp37m-win_amd64.whl.metadata (3.0 kB)
Requirement already satisfied: pyyaml in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from flask-ipban->anipose) (6.0)
Requirement already satisfied: requests in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from flask-ipban->anipose) (2.26.0)
Requirement already satisfied: python-dateutil>=2.7.3 in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from pandas->anipose) (2.9.0)
Requirement already satisfied: pytz>=2017.3 in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from pandas->anipose) (2024.2)
Requirement already satisfied: pillow in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from scikit-video->anipose) (9.2.0)
Requirement already satisfied: zipp>=0.5 in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from importlib-metadata->click->anipose) (3.6.0)
Requirement already satisfied: typing-extensions>=3.6.4 in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from importlib-metadata->click->anipose) (4.7.1)
Requirement already satisfied: MarkupSafe>=2.0 in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from Jinja2>=3.0->flask->anipose) (2.1.5)
Requirement already satisfied: six>=1.5 in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from python-dateutil>=2.7.3->pandas->anipose) (1.16.0)
Requirement already satisfied: llvmlite<0.40,>=0.39.0dev0 in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from numba->aniposelib>=0.7.0->anipose) (0.39.1)
Requirement already satisfied: setuptools in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from numba->aniposelib>=0.7.0->anipose) (59.8.0)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from requests->flask-ipban->anipose) (1.26.7)
Requirement already satisfied: certifi>=2017.4.17 in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from requests->flask-ipban->anipose) (2024.8.30)
Requirement already satisfied: charset-normalizer~=2.0.0 in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from requests->flask-ipban->anipose) (2.0.9)
Requirement already satisfied: idna<4,>=2.5 in c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages (from requests->flask-ipban->anipose) (3.3)
Downloading anipose-1.1.13-py3-none-any.whl (53 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.6/53.6 kB 2.7 MB/s eta 0:00:00
Downloading aniposelib-0.7.0-py3-none-any.whl (22 kB)
Downloading opencv_contrib_python-4.10.0.84-cp37-abi3-win_amd64.whl (45.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.5/45.5 MB 81.8 MB/s eta 0:00:00
Downloading Flask-2.2.5-py3-none-any.whl (101 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 101.8/101.8 kB ? eta 0:00:00
Downloading Flask_Compress-1.15-py3-none-any.whl (8.6 kB)
Downloading flask_ipban-1.1.5-py2.py3-none-any.whl (26 kB)
Downloading itsdangerous-2.1.2-py3-none-any.whl (15 kB)
Downloading Werkzeug-2.2.3-py3-none-any.whl (233 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.6/233.6 kB ? eta 0:00:00
Downloading Brotli-1.1.0-cp37-cp37m-win_amd64.whl (357 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 357.5/357.5 kB ? eta 0:00:00
Downloading zstandard-0.21.0-cp37-cp37m-win_amd64.whl (659 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 659.7/659.7 kB ? eta 0:00:00
Installing collected packages: brotli, zstandard, Werkzeug, opencv-contrib-python, itsdangerous, flask, aniposelib, flask-ipban, flask-compress, anipose
  Attempting uninstall: Werkzeug
    Found existing installation: Werkzeug 2.0.2
    Uninstalling Werkzeug-2.0.2:
      Successfully uninstalled Werkzeug-2.0.2
  Attempting uninstall: opencv-contrib-python
    Found existing installation: opencv-contrib-python 4.6.0.66
    Uninstalling opencv-contrib-python-4.6.0.66:
      Successfully uninstalled opencv-contrib-python-4.6.0.66
  Attempting uninstall: aniposelib
    Found existing installation: aniposelib 0.5.1
    Uninstalling aniposelib-0.5.1:
      Successfully uninstalled aniposelib-0.5.1
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
sleap-anipose 0.1.8 requires opencv-contrib-python<4.7.0, but you have opencv-contrib-python 4.10.0.84 which is incompatible.
Successfully installed Werkzeug-2.2.3 anipose-1.1.13 aniposelib-0.7.0 brotli-1.1.0 flask-2.2.5 flask-compress-1.15 flask-ipban-1.1.5 itsdangerous-2.1.2 opencv-contrib-python-4.10.0.84 zstandard-0.21.0

opencv error

(saa0) λ sleap-label
Traceback (most recent call last):
  File "C:\Users\TalmoLab\mambaforge\envs\saa0\Scripts\sleap-label-script.py", line 33, in <module>
    sys.exit(load_entry_point('sleap', 'console_scripts', 'sleap-label')())
  File "C:\Users\TalmoLab\mambaforge\envs\saa0\Scripts\sleap-label-script.py", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "C:\Users\TalmoLab\mambaforge\envs\saa0\lib\site-packages\importlib_metadata\__init__.py", line 209, in load
    module = import_module(match.group('module'))
  File "C:\Users\TalmoLab\mambaforge\envs\saa0\lib\importlib\__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 953, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 953, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\__init__.py", line 10, in <module>
    from sleap.io.dataset import Labels, load_file
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\io\dataset.py", line 66, in <module>
    from sleap.io.cameras import FrameGroup, RecordingSession
  File "d:\social-leap-estimates-animal-poses\source\sleap\sleap\io\cameras.py", line 11, in <module>
    from aniposelib.cameras import Camera, CameraGroup, FisheyeCamera
  File "C:\Users\TalmoLab\mambaforge\envs\saa0\lib\site-packages\aniposelib\__init__.py", line 6, in <module>
    from . import boards, cameras, utils
  File "C:\Users\TalmoLab\mambaforge\envs\saa0\lib\site-packages\aniposelib\boards.py", line 1, in <module>
    import cv2
  File "C:\Users\TalmoLab\mambaforge\envs\saa0\lib\site-packages\cv2\__init__.py", line 181, in <module>
    bootstrap()
  File "C:\Users\TalmoLab\mambaforge\envs\saa0\lib\site-packages\cv2\__init__.py", line 175, in bootstrap
    if __load_extra_py_code_for_module("cv2", submodule, DEBUG):
  File "C:\Users\TalmoLab\mambaforge\envs\saa0\lib\site-packages\cv2\__init__.py", line 28, in __load_extra_py_code_for_module
    py_module = importlib.import_module(module_name)
  File "C:\Users\TalmoLab\mambaforge\envs\saa0\lib\importlib\__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "C:\Users\TalmoLab\mambaforge\envs\saa0\lib\site-packages\cv2\gapi\__init__.py", line 323, in <module>
    cv.gapi.wip.GStreamerPipeline = cv.gapi_wip_gst_GStreamerPipeline
AttributeError: module 'cv2' has no attribute 'gapi_wip_gst_GStreamerPipeline'

find all flavors/versions of opencv

(saa0) λ pip freeze | grep opencv
opencv-contrib-python==4.10.0.84
opencv-python==4.6.0
opencv-python-headless==4.2.0.34

uninstall an opencv that was not installed by anipose

(saa0) λ pip uninstall opencv-contrib-python
Found existing installation: opencv-contrib-python 4.10.0.84
Uninstalling opencv-contrib-python-4.10.0.84:
  Would remove:
    c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages\cv2\*
    c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages\opencv_contrib_python-4.10.0.84.dist-info\*
  Would not remove (might be manually added):
    c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages\cv2\cv2.cp37-win_amd64.pyd
    c:\users\talmolab\mambaforge\envs\saa0\lib\site-packages\cv2\opencv_videoio_ffmpeg420_64.dll
Proceed (Y/n)?
  Successfully uninstalled opencv-contrib-python-4.10.0.84

sleap-label test

(saa0) λ sleap-label
Saving config: C:\Users\TalmoLab/.sleap/1.3.3/preferences.yaml
Restoring GUI state...

Software versions:
SLEAP: 1.3.3
TensorFlow: 2.7.0
Numpy: 1.21.5
Python: 3.7.12
OS: Windows-10-10.0.19041-SP0

Happy SLEAPing! :)
Saving config: C:\Users\TalmoLab/.sleap/1.3.3/preferences.yaml

anipose test

(saa0) λ anipose
Usage: anipose [OPTIONS] COMMAND [ARGS]...

Options:
  --version      Show the version and exit.
  --config FILE  The config file to use instead of the default "config.toml" .
  --help         Show this message and exit.

Commands:
  analyze
  angles
  calibrate
  calibration-errors
  convert-videos
  draw-calibration
  extract-frames
  filter
  filter-3d
  label-2d
  label-2d-filter
  label-2d-proj
  label-3d
  label-3d-filter
  label-combined
  label-filter-compare
  project-2d
  run-all
  run-data
  run-viz
  summarize-2d
  summarize-2d-filter
  summarize-3d
  summarize-errors
  tracking-errors
  train-autoencoder
  triangulate
  visualizer

We haven't personally done this, but let us know if it works for you. Even if you already have an existing SLEAP MV GUI environment, I would recommend creating another environment to install additional things in there instead of installing additional libraries to your existing environment.

Thanks,
Liezl

0 replies

martinesparza · 2024-10-02T12:28:18Z

martinesparza
Oct 2, 2024
Author

Hi @roomrys,

Thanks for the thorough answer. It was really helpful in helping me identify where the conflicts are, mainly related to opencv. I have done something slightly different to get it working which goes something like this:

# Create the environment called bnp and install sleap
$ conda create -y -n myenv -c conda-forge -c nvidia -c sleap -c anaconda sleap
$ conda activate myenv 

# Remove opencv pypi version because it conflicts with sleap-anipose
$ pip uninstall -y opencv-python-headless 

# Install required version
$ pip install "opencv-contrib-python<4.7.0" 

# Install sleap anipose and anipose version 1.0
$ pip install sleap_anipose
$ pip install "anipose<1.1"

Like this, everything seems to work (at least for now). I have also installed a version of anipose since I need one of their functions.

Maybe this is helpful for everyone!

Thanks,
Martín.

2 replies

80thelement Mar 12, 2025

you may have just saved me a year of tears. THANK YOU.

I'm new to all of this - why would you need all three SLEAP and SLEAP-anipose and anipose? What are the differences in their capabilities? I have not yet been able to find a comparison and am hoping this saves me the otherwise inevitable searching time.

Thanks again!!

martinesparza Mar 12, 2025
Author

Im glad I could help! Also, I think there have been some updates since this post and in our lab it seems like Anipose and Sleap_anipose were running with the default sleap install command (if you look on the main page).

As to why you need these, I can give you an example of what we do in the lab. We have multiple cameras tracking the position of several keypoints on a mouse. We use Sleap to have 2d predictions on each camera, and anipose to triangulate those 2d predictions into 3d positions in space. sleap_anipose is basically what connects the two!

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Integration of sleap with sleap-anipose and anipose #1973

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Integration of `sleap` with `sleap-anipose` and `anipose` #1973

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