Virginia9733
commented
3 years ago I have fixed this issue by using:
%%shell eval "$(conda shell.bash hook)" # copy conda command to shell conda activate VAME python
Now I could run the code in google colab,
NVIDIA-SMI 465.19.01
Driver Version: 460.32.03
CUDA Version: 11.2
Anaconda: Anaconda3-2020.02-Linux-x86_64.sh
python 3.7.10
Now I have successfully installed vame in the conda envirorment and could import vame. however, I faced the same issue as I mentioned in #46 , I could not create a training set.
Python 3.7.10 (default, Feb 26 2021, 18:47:35) [GCC 7.3.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information.
import vame Using CUDA GPU active: True GPU used: Tesla T4 config = vame.init_new_project(project='Muhang-VAME-Project', videos='/content/drive/MyDrive/VAME/video-1.mp4', working_directory='/content/drive/MyDrive/VAME/',videotype='.mp4') Created "/content/drive/MyDrive/VAME/Muhang-VAME-Project-May15-2021/videos" Created "/content/drive/MyDrive/VAME/Muhang-VAME-Project-May15-2021/data" Created "/content/drive/MyDrive/VAME/Muhang-VAME-Project-May15-2021/results" Created "/content/drive/MyDrive/VAME/Muhang-VAME-Project-May15-2021/model" No videos found in / Perhaps change the videotype, which is currently set to: .mp4 No videos found in / Perhaps change the videotype, which is currently set to: .mp4 No videos found in / Perhaps change the videotype, which is currently set to: .mp4 No videos found in / Perhaps change the videotype, which is currently set to: .mp4 No videos found in / Perhaps change the videotype, which is currently set to: .mp4 No videos found in . Perhaps change the videotype, which is currently set to: .mp4 Copying the videos
A VAME project has been created.
Now its time to prepare your data for VAME. The first step is to move your pose .csv file (e.g. DeepLabCut .csv) into the //YOUR//VAME//PROJECT//videos//pose_estimation folder. From here you can call either the function vame.egocentric_alignment() or if your data is by design egocentric call vame.csv_to_numpy(). This will prepare the data in .csv into the right format to start working with VAME.
config = '/content/drive/MyDrive/VAME/Muhang-VAME-Project-May15-2021/config.yaml' vame.update_config(config) ATTENTION! You are about to overwrite your current config.yaml. If you did changes, back up your current version and compare to the updated version. Do you want to continue? (yes/no)yes Your config.yaml has been updated. vame.egocentric_alignment(config, pose_ref_index=[0,5]) Your data is now ine right format and you can call vame.create_trainset() vame.create_trainset(config) Creating training dataset... Using robust setting to eliminate outliers! IQR factor: 4 Traceback (most recent call last): File "
", line 1, in File "/content/drive/My Drive/VAME/VAME-master/vame/model/create_training.py", line 186, in create_trainset traindata(cfg, files, cfg['test_fraction'], cfg['num_features'], cfg['savgol_filter']) File "/content/drive/My Drive/VAME/VAME-master/vame/model/create_training.py", line 66, in traindata X = np.concatenate(X_train, axis=0) File "<__array_function__ internals>", line 6, in concatenate ValueError: need at least one array to concatenate
pavolbauer
Hi,
I am currently trying to run VAME on my laptop without GPU. I could not create training data set as I mentioned in #46 I am wondering if it is possible to run VAME on google colab and use its GPU?
I tried to installed anaconda in colab and have successfully created the conda enviroment as followed:
from google.colab import drive drive.mount('/content/drive')
import os os.chdir("/content/drive/MyDrive/DeepLabCut_ROI/VAME")
!nvidia-smi
!wget https://repo.anaconda.com/archive/Anaconda3-5.2.0-Linux-x86_64.sh !bash Anaconda3-5.2.0-Linux-x86_64.sh -bfp /usr/local
import sys sys.path.insert(0, "/usr/local/lib/python3.7/site-packages/")
!conda env create -f VAME.yaml
!source activate VAME
However, when I tried to install vame on colab, I got the error message belowed: !python setup.py install
/usr/local/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'long_description_content_type' warnings.warn(msg) running install running bdist_egg running egg_info writing vame.egg-info/PKG-INFO writing dependency_links to vame.egg-info/dependency_links.txt writing entry points to vame.egg-info/entry_points.txt writing requirements to vame.egg-info/requires.txt writing top-level names to vame.egg-info/top_level.txt reading manifest file 'vame.egg-info/SOURCES.txt' writing manifest file 'vame.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/vame copying build/lib/vame/init.py -> build/bdist.linux-x86_64/egg/vame creating build/bdist.linux-x86_64/egg/vame/initialize_project copying build/lib/vame/initialize_project/new.py -> build/bdist.linux-x86_64/egg/vame/initialize_project copying build/lib/vame/initialize_project/init.py -> build/bdist.linux-x86_64/egg/vame/initialize_project creating build/bdist.linux-x86_64/egg/vame/util copying build/lib/vame/util/gif_pose_helper.py -> build/bdist.linux-x86_64/egg/vame/util copying build/lib/vame/util/csv_to_npy.py -> build/bdist.linux-x86_64/egg/vame/util copying build/lib/vame/util/init.py -> build/bdist.linux-x86_64/egg/vame/util copying build/lib/vame/util/align_egocentrical.py -> build/bdist.linux-x86_64/egg/vame/util copying build/lib/vame/util/auxiliary.py -> build/bdist.linux-x86_64/egg/vame/util creating build/bdist.linux-x86_64/egg/vame/model copying build/lib/vame/model/create_training.py -> build/bdist.linux-x86_64/egg/vame/model copying build/lib/vame/model/evaluate.py -> build/bdist.linux-x86_64/egg/vame/model copying build/lib/vame/model/dataloader.py -> build/bdist.linux-x86_64/egg/vame/model copying build/lib/vame/model/rnn_model.py -> build/bdist.linux-x86_64/egg/vame/model copying build/lib/vame/model/rnn_vae.py -> build/bdist.linux-x86_64/egg/vame/model copying build/lib/vame/model/init.py -> build/bdist.linux-x86_64/egg/vame/model creating build/bdist.linux-x86_64/egg/vame/analysis copying build/lib/vame/analysis/segment_behavior.py -> build/bdist.linux-x86_64/egg/vame/analysis copying build/lib/vame/analysis/tree_hierarchy.py -> build/bdist.linux-x86_64/egg/vame/analysis copying build/lib/vame/analysis/init.py -> build/bdist.linux-x86_64/egg/vame/analysis copying build/lib/vame/analysis/videowriter.py -> build/bdist.linux-x86_64/egg/vame/analysis copying build/lib/vame/analysis/umap_visualization.py -> build/bdist.linux-x86_64/egg/vame/analysis copying build/lib/vame/analysis/pose_segmentation.py -> build/bdist.linux-x86_64/egg/vame/analysis copying build/lib/vame/analysis/community_analysis.py -> build/bdist.linux-x86_64/egg/vame/analysis copying build/lib/vame/analysis/gif_creator.py -> build/bdist.linux-x86_64/egg/vame/analysis copying build/lib/vame/analysis/generative_functions.py -> build/bdist.linux-x86_64/egg/vame/analysis byte-compiling build/bdist.linux-x86_64/egg/vame/init.py to init.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/initialize_project/new.py to new.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/initialize_project/init.py to init.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/util/gif_pose_helper.py to gif_pose_helper.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/util/csv_to_npy.py to csv_to_npy.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/util/init.py to init.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/util/align_egocentrical.py to align_egocentrical.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/util/auxiliary.py to auxiliary.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/model/create_training.py to create_training.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/model/evaluate.py to evaluate.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/model/dataloader.py to dataloader.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/model/rnn_model.py to rnn_model.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/model/rnn_vae.py to rnn_vae.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/model/init.py to init.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/analysis/segment_behavior.py to segment_behavior.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/analysis/tree_hierarchy.py to tree_hierarchy.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/analysis/init.py to init.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/analysis/videowriter.py to videowriter.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/analysis/umap_visualization.py to umap_visualization.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/analysis/pose_segmentation.py to pose_segmentation.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/analysis/community_analysis.py to community_analysis.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/analysis/gif_creator.py to gif_creator.cpython-36.pyc byte-compiling build/bdist.linux-x86_64/egg/vame/analysis/generative_functions.py to generative_functions.cpython-36.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying vame.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying vame.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying vame.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying vame.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying vame.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying vame.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... creating 'dist/vame-1.0-py3.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing vame-1.0-py3.6.egg Copying vame-1.0-py3.6.egg to /usr/local/lib/python3.6/site-packages Adding vame 1.0 to easy-install.pth file Installing vame script to /usr/local/bin
Installed /usr/local/lib/python3.6/site-packages/vame-1.0-py3.6.egg Processing dependencies for vame==1.0 Searching for opencv-python Reading https://pypi.org/simple/opencv-python/ Downloading https://files.pythonhosted.org/packages/bb/08/9dbc183a3ac6baa95fabf749ddb531bd26256edfff5b6c2195eca26258e9/opencv-python-4.5.1.48.tar.gz#sha256=78a6db8467639383caedf1d111da3510a4ee1a0aacf2117821cae2ee8f92ce37 Best match: opencv-python 4.5.1.48 Processing opencv-python-4.5.1.48.tar.gz Writing /tmp/easy_install-9nd3ra8a/opencv-python-4.5.1.48/setup.cfg Running opencv-python-4.5.1.48/setup.py -q bdist_egg --dist-dir /tmp/easy_install-9nd3ra8a/opencv-python-4.5.1.48/egg-dist-tmp-loujmu5p Traceback (most recent call last): File "/usr/local/lib/python3.6/site-packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/usr/local/lib/python3.6/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/usr/local/lib/python3.6/site-packages/setuptools/sandbox.py", line 250, in run_setup _execfile(setup_script, ns) File "/usr/local/lib/python3.6/site-packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-9nd3ra8a/opencv-python-4.5.1.48/setup.py", line 10, in
entry_points={"console_scripts": "vame = vame:main"},
ModuleNotFoundError: No module named 'skbuild'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "setup.py", line 29, in
"opencv-python",
File "/usr/local/lib/python3.6/site-packages/setuptools/init.py", line 129, in setup
return distutils.core.setup(**attrs)
File "/usr/local/lib/python3.6/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/local/lib/python3.6/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/usr/local/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/usr/local/lib/python3.6/site-packages/setuptools/command/install.py", line 67, in run
self.do_egg_install()
File "/usr/local/lib/python3.6/site-packages/setuptools/command/install.py", line 117, in do_egg_install
cmd.run()
File "/usr/local/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 412, in run
self.easy_install(spec, not self.no_deps)
File "/usr/local/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 654, in easy_install
return self.install_item(None, spec, tmpdir, deps, True)
File "/usr/local/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 701, in install_item
self.process_distribution(spec, dist, deps)
File "/usr/local/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 746, in process_distribution
[requirement], self.local_index, self.easy_install
File "/usr/local/lib/python3.6/site-packages/pkg_resources/init.py", line 774, in resolve
replace_conflicting=replace_conflicting
File "/usr/local/lib/python3.6/site-packages/pkg_resources/init.py", line 1057, in best_match
return self.obtain(req, installer)
File "/usr/local/lib/python3.6/site-packages/pkg_resources/init.py", line 1069, in obtain
return installer(requirement)
File "/usr/local/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 673, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/usr/local/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 699, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/usr/local/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 884, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/usr/local/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 1152, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/usr/local/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 1138, in run_setup
run_setup(setup_script, args)
File "/usr/local/lib/python3.6/site-packages/setuptools/sandbox.py", line 253, in run_setup
raise
File "/usr/local/lib/python3.6/contextlib.py", line 99, in exit
self.gen.throw(type, value, traceback)
File "/usr/local/lib/python3.6/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/usr/local/lib/python3.6/contextlib.py", line 99, in exit
self.gen.throw(type, value, traceback)
File "/usr/local/lib/python3.6/site-packages/setuptools/sandbox.py", line 166, in save_modules
saved_exc.resume()
File "/usr/local/lib/python3.6/site-packages/setuptools/sandbox.py", line 141, in resume
six.reraise(type, exc, self._tb)
File "/usr/local/lib/python3.6/site-packages/setuptools/_vendor/six.py", line 685, in reraise
raise value.with_traceback(tb)
File "/usr/local/lib/python3.6/site-packages/setuptools/sandbox.py", line 154, in save_modules
yield saved
File "/usr/local/lib/python3.6/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/usr/local/lib/python3.6/site-packages/setuptools/sandbox.py", line 250, in run_setup
_execfile(setup_script, ns)
File "/usr/local/lib/python3.6/site-packages/setuptools/sandbox.py", line 45, in _execfile
exec(code, globals, locals)
File "/tmp/easy_install-9nd3ra8a/opencv-python-4.5.1.48/setup.py", line 10, in
entry_points={"console_scripts": "vame = vame:main"},
ModuleNotFoundError: No module named 'skbuild'