Questions - Githubissues

wweertman commented 3 years ago

Hey there!

Beautiful! just read your paper this looks fantastic. My study organism is octopus and we have had issues getting deeplabcut to differentiate the tips of their arms reliably. this creates lots of noise in the dataset which stops use from using tools like BSoiD effectively. This tool you have created looks like it might help and I am going to try including it in my workflow.

is this a good place to reach out with stupid questions and issues?

wweertman commented 3 years ago

Is there a way to incorporate already labelled dataset into your workflow and start training from a snapshot?

waq1129 commented 3 years ago

Hi, thanks a lot for your interest. Yes, you could use our package based on what you've already built upon DLC. If you have a project folder organized as data/Reaching-Mackenzie-2018-08-30, then you could run DGP in the terminal by following: python ['{DGP_DIR}/demo/run_dgp_demo.py'] --dlcpath "{PROJ_DIR}/task-scorer-date/" --shuffle 'the shuffle to run' --dlcsnapshot 'specify the DLC snapshot if you\'ve already run DLC with location refinement'

This command will allow you to run DGP continuing your DLC snapshot.

If you are new to our code, I would suggest installing the package as instructed and run with the demo dataset. If you successfully run it, then you can switch the project to your existing one.

wweertman commented 3 years ago

Awesome! I will give this a shot. Pretty stoked to see if this will improve our data to the point of being able to do behavioral segmentation.

Thank you

wweertman commented 3 years ago

install_pre_trained_resnet_error

So I got deepgraphpose downloaded. import deepgraphpose works and I can see the modules. Even got it working in spyder.

when I went to run

 C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose>curl http://download.tensorflow.org/models/resnet_v1_50_2016_08_28.tar.gz | tar xvz -C src/DeepLabCut/deeplabcut/pose_estimation_tensorflow/models/pretrained/

I got the error message

tar: Error opening archive: Failed to open '\\.\tape0'
 % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0 90.6M    0  4889    0     0   4889      0  5:24:06 --:--:--  5:24:06  8230
curl: (23) Failed writing body (607 != 1400)

looks like an error with downloading the pre-trained network for the demo..

I am going to give it a shot on my stuff following your directions above.

waq1129 commented 3 years ago

if you make a temporary folder say "tmp", will that work, i.e., curl http://download.tensorflow.org/models/resnet_v1_50_2016_08_28.tar.gz | tar xvz -C tmp

Mine is working. If yours is not working, there might be something wrong with curl I guess. If it works on your side, maybe you can manually copy what you download to this folder "src/DeepLabCut/deeplabcut/pose_estimation_tensorflow/models/pretrained/".

wweertman commented 3 years ago

okay doing that now. other note I tried pointing at one of my snapshots and I got an error related to the trainingfraction

(dlc-windowsGPU) C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose>python demo/run_dgp_demo.py --dlcpath "../MODELS/arms-weert-2021-01-17/" --shuffle 1 --dlcsnapshot 'dlc-models/iteration-7/armsJan17-transet80shuffle1/train/snapshot-1000000'
DLC loaded in light mode; you cannot use any GUI (labeling, relabeling and standalone GUI)
Project loaded in colab-mode. Apparently Colab has trouble loading statsmodels, so the smoothing & outlier frame extraction is disabled. Sorry!
Namespace(batch_size=10, dlcpath='../MODELS/arms-weert-2021-01-17/', dlcsnapshot="'dlc-models/iteration-7/armsJan17-transet80shuffle1/train/snapshot-1000000'", shuffle=1, test=False)

            ===============================================
            |                                             |
            |                                             |
            |    Running DGP with labeled frames only     |
            |                                             |
            |                                             |
            ===============================================

config_path ..\MODELS\arms-weert-2021-01-17\config.yaml
Traceback (most recent call last):
  File "demo/run_dgp_demo.py", line 206, in <module>
    step=1)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\models\fitdgp.py", line 339, in fit_dgp_labeledonly
    S0=S0)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 841, in __init__
    self.dlc_config = get_train_config(self.proj_config, shuffle)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\utils_model.py", line 93, in get_train_config
    TrainingFraction = cfg['TrainingFraction'][iteration]
IndexError: list index out of range

wweertman commented 3 years ago

if you make a temporary folder say "tmp", will that work, i.e., curl http://download.tensorflow.org/models/resnet_v1_50_2016_08_28.tar.gz | tar xvz -C tmp

Mine is working. If yours is not working, there might be something wrong with curl I guess. If it works on your side, maybe you can manually copy what you download to this folder "src/DeepLabCut/deeplabcut/pose_estimation_tensorflow/models/pretrained/".

I re-installed curl and made a temporary directory and ran the install command in that directory and got the same error. strange. I do not think it is a curl error. I think I should note that I am doing this through the anaconda prompt on windows 10.

from google searches of

curl: (23) Failure writing output to destination

the error message is vague.

waq1129 commented 3 years ago

Could you share your config.yaml?

wweertman commented 3 years ago

config.zip

waq1129 commented 3 years ago

In your config.yaml:

TrainingFraction:

0.8 iteration: 7

TrainingFraction = cfg['TrainingFraction'][iteration] this command looks for the 8th element in cfg['TrainingFraction'], that's why it throws the error. I would do TrainingFraction:

0.8
0.8
0.8
0.8
0.8
0.8
0.8
0.8 for a quick amendment (the display is problematic, so I share you the edited yaml file in the next reply)

waq1129 commented 3 years ago

config.yaml.zip

wweertman commented 3 years ago

okay got a new error. looks like a cuDNN error.

(dlc-windowsGPU) C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose>python demo/run_dgp_demo.py --dlcpath "../MODELS/arms-weert-2021-01-17/" --shuffle 1 --dlcsnapshot 'dlc-models/iteration-7/armsJan17-transet80shuffle1/train/snapshot-1000000'
DLC loaded in light mode; you cannot use any GUI (labeling, relabeling and standalone GUI)
Project loaded in colab-mode. Apparently Colab has trouble loading statsmodels, so the smoothing & outlier frame extraction is disabled. Sorry!
Namespace(batch_size=10, dlcpath='../MODELS/arms-weert-2021-01-17/', dlcsnapshot="'dlc-models/iteration-7/armsJan17-transet80shuffle1/train/snapshot-1000000'", shuffle=1, test=False)

            ===============================================
            |                                             |
            |                                             |
            |    Running DGP with labeled frames only     |
            |                                             |
            |                                             |
            ===============================================

config_path ..\MODELS\arms-weert-2021-01-17\config.yaml
C:\Users\wlwee\Documents\python\follow_cam_models\MODEL\arms-weert-2021-01-17\dlc-models\iteration-7\armsJan17-trainset80shuffle1\train\pose_cfg.yaml
Initializing ResNet
2021-02-17 19:16:19.046067: E tensorflow/stream_executor/cuda/cuda_dnn.cc:334] Could not create cudnn handle: CUDNN_STATUS_ALLOC_FAILED
2021-02-17 19:16:19.047281: E tensorflow/stream_executor/cuda/cuda_dnn.cc:334] Could not create cudnn handle: CUDNN_STATUS_ALLOC_FAILED
Traceback (most recent call last):
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 1334, in _do_call
    return fn(*args)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 1319, in _run_fn
    options, feed_dict, fetch_list, target_list, run_metadata)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 1407, in _call_tf_sessionrun
    run_metadata)
tensorflow.python.framework.errors_impl.UnknownError: Failed to get convolution algorithm. This is probably because cuDNN failed to initialize, so try looking to see if a warning log message was printed above.
         [[{{node resnet_v1_50/conv1/Conv2D}}]]

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "demo/run_dgp_demo.py", line 206, in <module>
    step=1)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\models\fitdgp.py", line 339, in fit_dgp_labeledonly
    S0=S0)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 853, in __init__
    self.datasets.append(Dataset(video_file, self.dlc_config, self.paths))
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 321, in __init__
    self.nx_out, self.ny_out = self._compute_pred_dims()  # x, y dims of model output
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 363, in _compute_pred_dims
    x_np = sess.run(x, feed_dict)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 929, in run
    run_metadata_ptr)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 1152, in _run
    feed_dict_tensor, options, run_metadata)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 1328, in _do_run
    run_metadata)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 1348, in _do_call
    raise type(e)(node_def, op, message)
tensorflow.python.framework.errors_impl.UnknownError: Failed to get convolution algorithm. This is probably because cuDNN failed to initialize, so try looking to see if a warning log message was printed above.
         [[node resnet_v1_50/conv1/Conv2D (defined at c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deeplabcut\deeplabcut\pose_estimation_tensorflow\nnet\pose_net.py:52) ]]

Caused by op 'resnet_v1_50/conv1/Conv2D', defined at:
  File "demo/run_dgp_demo.py", line 206, in <module>
    step=1)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\models\fitdgp.py", line 339, in fit_dgp_labeledonly
    S0=S0)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 853, in __init__
    self.datasets.append(Dataset(video_file, self.dlc_config, self.paths))
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 321, in __init__
    self.nx_out, self.ny_out = self._compute_pred_dims()  # x, y dims of model output
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 353, in _compute_pred_dims
    conv_inputs, end_points = pn.extract_features(inputs)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deeplabcut\deeplabcut\pose_estimation_tensorflow\nnet\pose_net.py", line 52, in extract_features
    global_pool=False, output_stride=self.cfg.output_stride,is_training=False)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\slim\python\slim\nets\resnet_v1.py", line 274, in resnet_v1_50
    scope=scope)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\slim\python\slim\nets\resnet_v1.py", line 205, in resnet_v1
    net = resnet_utils.conv2d_same(net, 64, 7, stride=2, scope='conv1')
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\slim\python\slim\nets\resnet_utils.py", line 146, in conv2d_same
    scope=scope)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\framework\python\ops\arg_scope.py", line 182, in func_with_args
    return func(*args, **current_args)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\layers\python\layers\layers.py", line 1155, in convolution2d
    conv_dims=2)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\framework\python\ops\arg_scope.py", line 182, in func_with_args
    return func(*args, **current_args)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\layers\python\layers\layers.py", line 1058, in convolution
    outputs = layer.apply(inputs)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\keras\engine\base_layer.py", line 1227, in apply
    return self.__call__(inputs, *args, **kwargs)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\layers\base.py", line 530, in __call__
    outputs = super(Layer, self).__call__(inputs, *args, **kwargs)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\keras\engine\base_layer.py", line 554, in __call__
    outputs = self.call(inputs, *args, **kwargs)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\keras\layers\convolutional.py", line 194, in call
    outputs = self._convolution_op(inputs, self.kernel)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\ops\nn_ops.py", line 966, in __call__
    return self.conv_op(inp, filter)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\ops\nn_ops.py", line 591, in __call__
    return self.call(inp, filter)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\ops\nn_ops.py", line 208, in __call__
    name=self.name)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\ops\gen_nn_ops.py", line 1026, in conv2d
    data_format=data_format, dilations=dilations, name=name)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\framework\op_def_library.py", line 788, in _apply_op_helper
    op_def=op_def)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\util\deprecation.py", line 507, in new_func
    return func(*args, **kwargs)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\framework\ops.py", line 3300, in create_op
    op_def=op_def)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\framework\ops.py", line 1801, in __init__
    self._traceback = tf_stack.extract_stack()

UnknownError (see above for traceback): Failed to get convolution algorithm. This is probably because cuDNN failed to initialize, so try looking to see if a warning log message was printed above.
         [[node resnet_v1_50/conv1/Conv2D (defined at c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deeplabcut\deeplabcut\pose_estimation_tensorflow\nnet\pose_net.py:52) ]]

waq1129 commented 3 years ago

if you make a temporary folder say "tmp", will that work, i.e., curl http://download.tensorflow.org/models/resnet_v1_50_2016_08_28.tar.gz | tar xvz -C tmp Mine is working. If yours is not working, there might be something wrong with curl I guess. If it works on your side, maybe you can manually copy what you download to this folder "src/DeepLabCut/deeplabcut/pose_estimation_tensorflow/models/pretrained/".

I re-installed curl and made a temporary directory and ran the install command in that directory and got the same error. strange. I do not think it is a curl error. I think I should note that I am doing this through the anaconda prompt on windows 10.

from google searches of

curl: (23) Failure writing output to destination

the error message is vague.

Any possibility making curl work on windows? Sorry that I have no experience working with windows. If it still not works, I would say just manually download resnet_v1_50_2016_08_28.tar.gz and unzip it and put it in the target folder. It's really just what that command does.

wweertman commented 3 years ago

if you make a temporary folder say "tmp", will that work, i.e., curl http://download.tensorflow.org/models/resnet_v1_50_2016_08_28.tar.gz | tar xvz -C tmp Mine is working. If yours is not working, there might be something wrong with curl I guess. If it works on your side, maybe you can manually copy what you download to this folder "src/DeepLabCut/deeplabcut/pose_estimation_tensorflow/models/pretrained/".

I re-installed curl and made a temporary directory and ran the install command in that directory and got the same error. strange. I do not think it is a curl error. I think I should note that I am doing this through the anaconda prompt on windows 10. from google searches of

curl: (23) Failure writing output to destination

the error message is vague.

Any possibility making curl work on windows? Sorry that I have no experience working with windows. If it still not works, I would say just manually download resnet_v1_50_2016_08_28.tar.gz and unzip it and put it in the target folder. It's really just what that command does.

yeah I was going to manually do it. First I am testing if I can do some deeplabcut stuff in the environment that involves downloading the resnet. I've had no issues with curl before. I compared paths with the paths deeplabcut uses and there is no issue there.

waq1129 commented 3 years ago

okay got a new error. looks like a cuDNN error.

(dlc-windowsGPU) C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose>python demo/run_dgp_demo.py --dlcpath "../MODELS/arms-weert-2021-01-17/" --shuffle 1 --dlcsnapshot 'dlc-models/iteration-7/armsJan17-transet80shuffle1/train/snapshot-1000000'
DLC loaded in light mode; you cannot use any GUI (labeling, relabeling and standalone GUI)
Project loaded in colab-mode. Apparently Colab has trouble loading statsmodels, so the smoothing & outlier frame extraction is disabled. Sorry!
Namespace(batch_size=10, dlcpath='../MODELS/arms-weert-2021-01-17/', dlcsnapshot="'dlc-models/iteration-7/armsJan17-transet80shuffle1/train/snapshot-1000000'", shuffle=1, test=False)

            ===============================================
            |                                             |
            |                                             |
            |    Running DGP with labeled frames only     |
            |                                             |
            |                                             |
            ===============================================

config_path ..\MODELS\arms-weert-2021-01-17\config.yaml
C:\Users\wlwee\Documents\python\follow_cam_models\MODEL\arms-weert-2021-01-17\dlc-models\iteration-7\armsJan17-trainset80shuffle1\train\pose_cfg.yaml
Initializing ResNet
2021-02-17 19:16:19.046067: E tensorflow/stream_executor/cuda/cuda_dnn.cc:334] Could not create cudnn handle: CUDNN_STATUS_ALLOC_FAILED
2021-02-17 19:16:19.047281: E tensorflow/stream_executor/cuda/cuda_dnn.cc:334] Could not create cudnn handle: CUDNN_STATUS_ALLOC_FAILED
Traceback (most recent call last):
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 1334, in _do_call
    return fn(*args)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 1319, in _run_fn
    options, feed_dict, fetch_list, target_list, run_metadata)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 1407, in _call_tf_sessionrun
    run_metadata)
tensorflow.python.framework.errors_impl.UnknownError: Failed to get convolution algorithm. This is probably because cuDNN failed to initialize, so try looking to see if a warning log message was printed above.
         [[{{node resnet_v1_50/conv1/Conv2D}}]]

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "demo/run_dgp_demo.py", line 206, in <module>
    step=1)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\models\fitdgp.py", line 339, in fit_dgp_labeledonly
    S0=S0)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 853, in __init__
    self.datasets.append(Dataset(video_file, self.dlc_config, self.paths))
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 321, in __init__
    self.nx_out, self.ny_out = self._compute_pred_dims()  # x, y dims of model output
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 363, in _compute_pred_dims
    x_np = sess.run(x, feed_dict)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 929, in run
    run_metadata_ptr)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 1152, in _run
    feed_dict_tensor, options, run_metadata)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 1328, in _do_run
    run_metadata)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\client\session.py", line 1348, in _do_call
    raise type(e)(node_def, op, message)
tensorflow.python.framework.errors_impl.UnknownError: Failed to get convolution algorithm. This is probably because cuDNN failed to initialize, so try looking to see if a warning log message was printed above.
         [[node resnet_v1_50/conv1/Conv2D (defined at c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deeplabcut\deeplabcut\pose_estimation_tensorflow\nnet\pose_net.py:52) ]]

Caused by op 'resnet_v1_50/conv1/Conv2D', defined at:
  File "demo/run_dgp_demo.py", line 206, in <module>
    step=1)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\models\fitdgp.py", line 339, in fit_dgp_labeledonly
    S0=S0)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 853, in __init__
    self.datasets.append(Dataset(video_file, self.dlc_config, self.paths))
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 321, in __init__
    self.nx_out, self.ny_out = self._compute_pred_dims()  # x, y dims of model output
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 353, in _compute_pred_dims
    conv_inputs, end_points = pn.extract_features(inputs)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deeplabcut\deeplabcut\pose_estimation_tensorflow\nnet\pose_net.py", line 52, in extract_features
    global_pool=False, output_stride=self.cfg.output_stride,is_training=False)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\slim\python\slim\nets\resnet_v1.py", line 274, in resnet_v1_50
    scope=scope)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\slim\python\slim\nets\resnet_v1.py", line 205, in resnet_v1
    net = resnet_utils.conv2d_same(net, 64, 7, stride=2, scope='conv1')
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\slim\python\slim\nets\resnet_utils.py", line 146, in conv2d_same
    scope=scope)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\framework\python\ops\arg_scope.py", line 182, in func_with_args
    return func(*args, **current_args)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\layers\python\layers\layers.py", line 1155, in convolution2d
    conv_dims=2)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\framework\python\ops\arg_scope.py", line 182, in func_with_args
    return func(*args, **current_args)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\contrib\layers\python\layers\layers.py", line 1058, in convolution
    outputs = layer.apply(inputs)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\keras\engine\base_layer.py", line 1227, in apply
    return self.__call__(inputs, *args, **kwargs)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\layers\base.py", line 530, in __call__
    outputs = super(Layer, self).__call__(inputs, *args, **kwargs)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\keras\engine\base_layer.py", line 554, in __call__
    outputs = self.call(inputs, *args, **kwargs)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\keras\layers\convolutional.py", line 194, in call
    outputs = self._convolution_op(inputs, self.kernel)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\ops\nn_ops.py", line 966, in __call__
    return self.conv_op(inp, filter)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\ops\nn_ops.py", line 591, in __call__
    return self.call(inp, filter)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\ops\nn_ops.py", line 208, in __call__
    name=self.name)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\ops\gen_nn_ops.py", line 1026, in conv2d
    data_format=data_format, dilations=dilations, name=name)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\framework\op_def_library.py", line 788, in _apply_op_helper
    op_def=op_def)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\util\deprecation.py", line 507, in new_func
    return func(*args, **kwargs)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\framework\ops.py", line 3300, in create_op
    op_def=op_def)
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\tensorflow\python\framework\ops.py", line 1801, in __init__
    self._traceback = tf_stack.extract_stack()

UnknownError (see above for traceback): Failed to get convolution algorithm. This is probably because cuDNN failed to initialize, so try looking to see if a warning log message was printed above.
         [[node resnet_v1_50/conv1/Conv2D (defined at c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deeplabcut\deeplabcut\pose_estimation_tensorflow\nnet\pose_net.py:52) ]]

Find a possible reason and solution for this: https://github.com/tensorflow/tensorflow/issues/24828#issuecomment-457425190

wweertman commented 3 years ago

(dlc-windowsGPU) C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose>conda list cudnn
# packages in environment at C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU:
#
# Name                    Version                   Build  Channel
cudnn                     7.6.5                cuda10.0_0

import tensorflow as tf

tf.version.VERSION
'1.13.1'

hey there sorry for the long response time. had to help a student with a R issue and eat dinner. these are my builds that seem relevant to this issue thread. seems like the general solve is to downgrade the tensorflow version.

I think 1.13.1 is not required for deeplabcut i think it can go back a few versions. not sure about cuDNN. What about deepgraphpose?

waq1129 commented 3 years ago

I think there is some version requirement for TF but honestly, I do have multiple version installed on my end for different virtual environments. You can try 1.9.0 to see whether that works with your cudnn.

wweertman commented 3 years ago

(dlc-windowsGPU) C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose>conda list cudnn
# packages in environment at C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU:
#
# Name                    Version                   Build  Channel
cudnn                     7.6.5                cuda10.0_0
import tensorflow as tf

tf.version.VERSION
'1.13.1'
hey there sorry for the long response time. had to help a student with a R issue and eat dinner. these are my builds that seem relevant to this issue thread. seems like the general solve is to downgrade the tensorflow version.

I think 1.13.1 is not required for deeplabcut i think it can go back a few versions. not sure about cuDNN. What about deepgraphpose?

GPU

I have an ubuntu machine i can try doing this work on at campus. I will try following this there.

wweertman commented 3 years ago

whoops.

alright.. so.. I literally changed nothing. just closed some other python instances I had going and re-ran what I ran before.

(dlc-windowsGPU) C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose>python demo/run_dgp_demo.py --dlcpath "../MODELS/arms-weert-2021-01-17/" --shuffle 1 --dlcsnapshot 'dlc-models/iteration-7/armsJan17-transet80shuffle1/train/snapshot-1000000'
DLC loaded in light mode; you cannot use any GUI (labeling, relabeling and standalone GUI)
Project loaded in colab-mode. Apparently Colab has trouble loading statsmodels, so the smoothing & outlier frame extraction is disabled. Sorry!
Namespace(batch_size=10, dlcpath='../MODELS/arms-weert-2021-01-17/', dlcsnapshot="'dlc-models/iteration-7/armsJan17-transet80shuffle1/train/snapshot-1000000'", shuffle=1, test=False)

            ===============================================
            |                                             |
            |                                             |
            |    Running DGP with labeled frames only     |
            |                                             |
            |                                             |
            ===============================================

config_path ..\MODELS\arms-weert-2021-01-17\config.yaml
C:\Users\wlwee\Documents\python\follow_cam_models\MODEL\arms-weert-2021-01-17\dlc-models\iteration-7\armsJan17-trainset80shuffle1\train\pose_cfg.yaml
Initializing ResNet
Traceback (most recent call last):
  File "demo/run_dgp_demo.py", line 206, in <module>
    step=1)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\models\fitdgp.py", line 339, in fit_dgp_labeledonly
    S0=S0)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 853, in __init__
    self.datasets.append(Dataset(video_file, self.dlc_config, self.paths))
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 327, in __init__
    idxs_train = get_frame_idxs_from_train_mat(data, self.video_name)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 276, in get_frame_idxs_from_train_mat
    idx = int(dat[0][0].rsplit('/', 1)[-1][3:].split('.')[0])
ValueError: invalid literal for int() with base 10: 'eled-data\\2908_3021_fc\\img051'

waq1129 commented 3 years ago

whoops.

alright.. so.. I literally changed nothing. just closed some other python instances I had going and re-ran what I ran before.

(dlc-windowsGPU) C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose>python demo/run_dgp_demo.py --dlcpath "../MODELS/arms-weert-2021-01-17/" --shuffle 1 --dlcsnapshot 'dlc-models/iteration-7/armsJan17-transet80shuffle1/train/snapshot-1000000'
DLC loaded in light mode; you cannot use any GUI (labeling, relabeling and standalone GUI)
Project loaded in colab-mode. Apparently Colab has trouble loading statsmodels, so the smoothing & outlier frame extraction is disabled. Sorry!
Namespace(batch_size=10, dlcpath='../MODELS/arms-weert-2021-01-17/', dlcsnapshot="'dlc-models/iteration-7/armsJan17-transet80shuffle1/train/snapshot-1000000'", shuffle=1, test=False)

            ===============================================
            |                                             |
            |                                             |
            |    Running DGP with labeled frames only     |
            |                                             |
            |                                             |
            ===============================================

config_path ..\MODELS\arms-weert-2021-01-17\config.yaml
C:\Users\wlwee\Documents\python\follow_cam_models\MODEL\arms-weert-2021-01-17\dlc-models\iteration-7\armsJan17-trainset80shuffle1\train\pose_cfg.yaml
Initializing ResNet
Traceback (most recent call last):
  File "demo/run_dgp_demo.py", line 206, in <module>
    step=1)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\models\fitdgp.py", line 339, in fit_dgp_labeledonly
    S0=S0)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 853, in __init__
    self.datasets.append(Dataset(video_file, self.dlc_config, self.paths))
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 327, in __init__
    idxs_train = get_frame_idxs_from_train_mat(data, self.video_name)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 276, in get_frame_idxs_from_train_mat
    idx = int(dat[0][0].rsplit('/', 1)[-1][3:].split('.')[0])
ValueError: invalid literal for int() with base 10: 'eled-data\\2908_3021_fc\\img051'

is "eled-data\2908_3021_fc\img051" the path to your data? Sorry that we have never tested on a windows machine. So we didn't take these windows format into consideration. It would be great if you could switch to a ubuntu. Apologize for causing this inconvenience. It will take us some time to fix it on windows.

wweertman commented 3 years ago

if you make a temporary folder say "tmp", will that work, i.e., curl http://download.tensorflow.org/models/resnet_v1_50_2016_08_28.tar.gz | tar xvz -C tmp Mine is working. If yours is not working, there might be something wrong with curl I guess. If it works on your side, maybe you can manually copy what you download to this folder "src/DeepLabCut/deeplabcut/pose_estimation_tensorflow/models/pretrained/".

I re-installed curl and made a temporary directory and ran the install command in that directory and got the same error. strange. I do not think it is a curl error. I think I should note that I am doing this through the anaconda prompt on windows 10. from google searches of

curl: (23) Failure writing output to destination

the error message is vague.

Any possibility making curl work on windows? Sorry that I have no experience working with windows. If it still not works, I would say just manually download resnet_v1_50_2016_08_28.tar.gz and unzip it and put it in the target folder. It's really just what that command does.

I manually downloaded the pre-trained model then ran

(dlc-windowsGPU) C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose>python demo/run_dgp_demo.py --dlcpath data/Reaching-Mackenzie-2018-08-30

I got a strange error KeyError 'videos/reachingvideo1.avi'

DLC loaded in light mode; you cannot use any GUI (labeling, relabeling and standalone GUI)
Project loaded in colab-mode. Apparently Colab has trouble loading statsmodels, so the smoothing & outlier frame extraction is disabled. Sorry!
Namespace(batch_size=10, dlcpath='data/Reaching-Mackenzie-2018-08-30', dlcsnapshot=None, shuffle=1, test=False)

here is the path to dlc
data/Reaching-Mackenzie-2018-08-30
working dir is
C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose

project path is
C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose\data/Reaching-Mackenzie-2018-08-30
video is here
C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose\data/Reaching-Mackenzie-2018-08-30\videos\reachingvideo1.avi
video sets are
{'C:\\Users\\wlwee\\Documents\\python\\DGP_models\\deepgraphpose\\data\\Reaching-Mackenzie-2018-08-30\\videos\\reachingvideo1.avi': {'crop': '0, 832, 0, 747'}}

Traceback (most recent call last):
  File "demo/run_dgp_demo.py", line 169, in <module>
    dlcpath = update_config_files(dlcpath)
  File "demo/run_dgp_demo.py", line 54, in update_config_files
    yaml_cfg['video_sets'][video_loc] = yaml_cfg['video_sets'].pop('videos/reachingvideo1.avi')
KeyError: 'videos/reachingvideo1.avi'

I added some print statements and it all seems fine.. this is the culprit line of code

yaml_cfg['video_sets'][video_loc] = yaml_cfg['video_sets'].pop('videos/reachingvideo1.avi')

I am not that familiar with the yaml library. I built a function using it awhile ago to iteratively evaluate deeplabcut models but that's it.

It is something to do with the

.pop('videos/reachingvideo1.avi')

which i am basically just has something to do with populating a .yaml

waq1129 commented 3 years ago

The same issue, the path format is written for Linux by default.

wweertman commented 3 years ago

The same issue, the path format is written for Linux by default.

AH! yes that makes so much sense. I started commenting out lines of code and just iteratively rerunning the script. It seems like every error is a path error.

It looks like your handling of the paths is fine. The os library automatically formats it in a windows friendly way I think it has something to do with how the yaml library is formating the paths. And possibly how the paths are formated within the .yaml file

The script failed at this line a few times.

yaml_cfg['video_sets'][video_loc] = yaml_cfg['video_sets'].pop('videos/reachingvideo1.avi')

Well that's the joy of crowd testing software right?

waq1129 commented 3 years ago

Yeah, thanks for your patience to go through these errors. This provides us a lot of useful feedbacks.

wweertman commented 3 years ago

The same issue, the path format is written for Linux by default.

AH! yes that makes so much sense. I started commenting out lines of code and just iteratively rerunning the script. It seems like every error is a path error.

It looks like your handling of the paths is fine. The os library automatically formats it in a windows friendly way I think it has something to do with how the yaml library is formating the paths. And possibly how the paths are formated within the .yaml file

The script failed at this line a few times.

yaml_cfg['video_sets'][video_loc] = yaml_cfg['video_sets'].pop('videos/reachingvideo1.avi')

Well that's the joy of crowd testing software right?

manual correction of the .yaml file format does nothing

waq1129 commented 3 years ago

Change videos/reachingvideo1.avi into windows format in the code?

wweertman commented 3 years ago

Yeah, thanks for your patience to go through these errors. This provides us a lot of useful feedbacks.

happy to help!! Tomorrow or Friday I will go and set up the ubuntu machine in lab so I can work on it from home and see if I can get the stuff to work. Cheers! Have a good night. thanks for help, hope it gets figured out. As much as I love ubuntu

Change videos/reachingvideo1.avi into windows format in the code?

I have changed it to every possible format I can think of and the same error still happens.

Then maybe use this full path starting from C:

yaml_cfg['video_sets'][video_loc] = yaml_cfg['video_sets'].pop('C:/Users/wlwee/Documents/python/DGP_models/deepgraphpose/data/Reaching-Mackenzie-2018-08-30/videos/reachingvideo1.avi')

that bumped it past the error

waq1129 commented 3 years ago

Interesting, can you print out yaml_cfg[‘video_set’] and see what happens?

wweertman commented 3 years ago

video sets are
{'C:/Users/wlwee/Documents/python/DGP_models/deepgraphpose/data/Reaching-Mackenzie-2018-08-30/videos/reachingvideo1.avi': {'crop': '0, 832, 0, 747'}}

wweertman commented 3 years ago

the weird thing is that its a KeyError


  File "demo/run_dgp_demo.py", line 174, in <module>
    dlcpath = update_config_files(dlcpath)
  File "demo/run_dgp_demo.py", line 59, in update_config_files
    yaml_cfg['video_sets'][video_loc] = yaml_cfg['video_sets'].pop('videos/reachingvideo1.avi')
KeyError: 'videos/reachingvideo1.avi'```

waq1129 commented 3 years ago

Then maybe use this full path starting from C:

waq1129 commented 3 years ago

The default working path should be in Reaching-xxx, that’s why we can use the relative path. It would be worth checking that.

wweertman commented 3 years ago

Then maybe use this full path starting from C:

yaml_cfg['video_sets'][video_loc] = yaml_cfg['video_sets'].pop('C:/Users/wlwee/Documents/python/DGP_models/deepgraphpose/data/Reaching-Mackenzie-2018-08-30/videos/reachingvideo1.avi')

bumped it past the error

wweertman commented 3 years ago

oh man okay so I put

os.chdir = 'C:/Users/wlwee/Documents/python/DGP_models/deepgraphpose/data/Reaching-Mackenzie-2018-08-30'

and the script progressed quite aways before encountering another path error

wweertman commented 3 years ago

oh man okay so I put
os.chdir ('C:/Users/wlwee/Documents/python/DGP_models/deepgraphpose/data/Reaching-Mackenzie-2018-08-30')
and the script progressed quite aways before encountering another path error

so I do not think it is the yaml library.

wweertman commented 3 years ago

(dlc-windowsGPU) C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose>python demo/run_dgp_demo.py --dlcpath data/Reaching-Mackenzie-2018-08-30 --shuffle 1 --dlcsnapshot src/DeepLabCut/deeplabcut/pose_estimation_tensorflow/models/pretrained/resnet_v1_50.ckpt
DLC loaded in light mode; you cannot use any GUI (labeling, relabeling and standalone GUI)
Project loaded in colab-mode. Apparently Colab has trouble loading statsmodels, so the smoothing & outlier frame extraction is disabled. Sorry!
Namespace(batch_size=10, dlcpath='data/Reaching-Mackenzie-2018-08-30', dlcsnapshot='src/DeepLabCut/deeplabcut/pose_estimation_tensorflow/models/pretrained/resnet_v1_50.ckpt', shuffle=1, test=False)

here is the path to dlc
data/Reaching-Mackenzie-2018-08-30
working dir is
C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose

project path is
C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose\data/Reaching-Mackenzie-2018-08-30
exists
video is here
C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose\data/Reaching-Mackenzie-2018-08-30\videos\reachingvideo1.avi
exists
video sets are
{'videos/reachingvideo1.avi': {'crop': '0, 832, 0, 747'}}

            ===============================================
            |                                             |
            |                                             |
            |    Running DGP with labeled frames only     |
            |                                             |
            |                                             |
            ===============================================

config_path C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose\data\Reaching-Mackenzie-2018-08-30\config.yaml
C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose\data\Reaching-Mackenzie-2018-08-30\dlc-models\iteration-0\ReachingAug30-trainset95shuffle1\train\pose_cfg.yaml
Warning. Check the number of frames
Warning. Check the number of frames
Initializing ResNet
reachingvideo1
[  5  20  23  28  31  33  36  37  38  40  42  46  48  52  60  68  71  75
  77  80  87  90 100 103 108 118 119 126 141 142 145 151 152 157 167 168
 177 179 180 194 211 213 214 225 227 228 230 231 234 237 240 245]

Creating training datasets
--------------------------
Selected additional 0 hidden frames
Skipped 0 high motion energy (me) frames since in visible window or close to higher me hidden frame
Traceback (most recent call last):
  File "demo/run_dgp_demo.py", line 232, in <module>
    step=1)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\models\fitdgp.py", line 367, in fit_dgp_labeledonly
    data_batcher.create_batches_from_resnet_output(snapshot, **batch_dict)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 922, in create_batches_from_resnet_output
    dataset.create_batches_from_resnet_output(self.batch_info, self.paths['batched_data'])
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 389, in create_batches_from_resnet_output
    pv_idxs, ph_idxs = self._process_video(batch_info)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 425, in _process_video
    ph_idxs = self._find_good_hidden_frames(pv_idxs, batch_info)
  File "c:\users\wlwee\documents\python\dgp_models\deepgraphpose\src\deepgraphpose\dataset.py", line 549, in _find_good_hidden_frames
    np.save(idxs_file, {'pv': pv_idxs, 'ph': ph_idxs_sel})
  File "C:\Users\wlwee\Anaconda3\envs\dlc-windowsGPU\lib\site-packages\numpy\lib\npyio.py", line 524, in save
    fid = open(file, "wb")
FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\wlwee\\Documents\\python\\DGP_models\\deepgraphpose\\data\\Reaching-Mackenzie-2018-08-30\\dlc-models\\iteration-0\\ReachingAug30-trainset95shuffle1\\train\\batched_data\\snapshot-0\\Reaching-Mackenzie-2018-08-30\\videos\\reachingvideo1__nsjump=None_step=1_ns=10_nc=2048_max=2000_idxs.npy'

here is where it got to

waq1129 commented 3 years ago

Something you changed earlier might affect here, it should be C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose\data\Reaching-Mackenzie-2018-08-30\dlc-models\iteration-0\ReachingAug30-trainset95shuffle1\train\batched_data\snapshot-0\reachingvideo1__nsjump=None_step=1_ns=10_nc=2048_max=2000_idxs.npy' or something like that. You might be able to find it in snapshot-0 folder

wweertman commented 3 years ago

Something you changed earlier might affect here, it should be C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose\data\Reaching-Mackenzie-2018-08-30\dlc-models\iteration-0\ReachingAug30-trainset95shuffle1\train\batched_data\snapshot-0\reachingvideo1__nsjump=None_step=1_ns=10_nc=2048_max=2000_idxs.npy' or something like that. You might be able to find it in snapshot-0 folder

oh man that folder is empty. not entirely sure what a .npy file is. I am going to re-download the project so I have a fresh copy of the demo to work on.

wweertman commented 3 years ago

Something you changed earlier might affect here, it should be C:\Users\wlwee\Documents\python\DGP_models\deepgraphpose\data\Reaching-Mackenzie-2018-08-30\dlc-models\iteration-0\ReachingAug30-trainset95shuffle1\train\batched_data\snapshot-0\reachingvideo1__nsjump=None_step=1_ns=10_nc=2048_max=2000_idxs.npy' or something like that. You might be able to find it in snapshot-0 folder

oh man that folder is empty. not entirely sure what a .npy file is. I am going to re-download the project so I have a fresh copy of the demo to work on.

numpy file format https://fileinfo.com/extension/npy#:~:text=An%20NPY%20file%20is%20a,includes%20dtype%20and%20shape%20information.

waq1129 commented 3 years ago

If you can print idxs_file before np.save(idxs_file, {'pv': pv_idxs, 'ph': ph_idxs_sel}), that might tell you the path you save the npy file. I think something is wrong when saving that file. That’s why you see nothing there.

wweertman commented 3 years ago

If you can print idxs_file before np.save(idxs_file, {'pv': pv_idxs, 'ph': ph_idxs_sel}), that might tell you the path you save the npy file. I think something is wrong when saving that file. That’s why you see nothing there.

where is this in the script? Ctrl + F finds nothing

wweertman commented 3 years ago

If you can print idxs_file before np.save(idxs_file, {'pv': pv_idxs, 'ph': ph_idxs_sel}), that might tell you the path you save the npy file. I think something is wrong when saving that file. That’s why you see nothing there.

where is this in the script? Ctrl + F finds nothing

oh stupid question its in another script

wweertman commented 3 years ago

okay well. The KeyError returned. I got it to run once with a print statement where you wanted it. I added some extra print() around it and ran again and the KeyError popped up.

wweertman commented 3 years ago

okay well. The KeyError returned. I got it to run once with a print statement where you wanted it. I added some extra print() around it and ran again and the KeyError popped up.

I think my little head is going to explode. I am going to get ready to sleep now.

wweertman commented 3 years ago

okay well. The KeyError returned. I got it to run once with a print statement where you wanted it. I added some extra print() around it and ran again and the KeyError popped up.

I think my little head is going to explode. I am going to get ready to sleep now.

Traceback (most recent call last):
  File "demo/run_dgp_demo.py", line 175, in <module>
    dlcpath = update_config_files(dlcpath)
  File "demo/run_dgp_demo.py", line 60, in update_config_files
    yaml_cfg['video_sets'][video_loc] = yaml_cfg['video_sets'].pop(video_loc)
KeyError: 'C:\\Users\\wlwee\\Documents\\python\\DGP_models\\deepgraphpose\\data/Reaching-Mackenzie-2018-08-30\\videos\\reachingvideo1.avi'

wweertman commented 3 years ago

(base) weertman@weertman-Z270P-D3:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 18.04.4 LTS
Release:    18.04
Codename:   bionic

hey there I am back! I tried to get it working on the ubuntu machine and got a tensorflow error see below where I got to.

I followed your instructions, when I imported deeplabcut the tensorflow error thrown.

(base) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS$ git clone https://github.com/paninski-lab/deepgraphpose.git
Cloning into 'deepgraphpose'...
remote: Enumerating objects: 47, done.
remote: Counting objects: 100% (47/47), done.
remote: Compressing objects: 100% (33/33), done.
remote: Total 459 (delta 25), reused 28 (delta 14), pack-reused 412
Receiving objects: 100% (459/459), 71.15 MiB | 10.35 MiB/s, done.
Resolving deltas: 100% (67/67), done.
(base) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS$ cd deepgraphpose/
(base) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose$ cd src/
(base) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut$ cd conda-environments/
(base) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/conda-environments$ ls
dgp-macOS-CPU.yaml   dlc-macOS-CPU.yaml   dlc-windowsCPU.yaml  README.md
dgp-ubuntu-GPU.yaml  dlc-ubuntu-GPU.yaml  dlc-windowsGPU.yaml
(base) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/conda-environments$ conda env create -f dgp-ubuntu-GPU.yaml 
Collecting package metadata (repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.9.2

Please update conda by running

    $ conda update -n base -c defaults conda

Downloading and Extracting Packages
sqlite-3.33.0        | 1.1 MB    | ######################################################## | 100% 
openssl-1.1.1j       | 2.5 MB    | ######################################################## | 100% 
ca-certificates-2021 | 121 KB    | ######################################################## | 100% 
libffi-3.2.1         | 48 KB     | ######################################################## | 100% 
setuptools-52.0.0    | 724 KB    | ######################################################## | 100% 
wheel-0.36.2         | 33 KB     | ######################################################## | 100% 
certifi-2020.12.5    | 140 KB    | ######################################################## | 100% 
libedit-3.1.20191231 | 116 KB    | ######################################################## | 100% 
pip-21.0.1           | 1.8 MB    | ######################################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Ran pip subprocess with arguments:
['/home/weertman/anaconda3/envs/dgp/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/weertman/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/conda-environments/condaenv.izm11_wo.requirements.txt']
Pip subprocess output:
Collecting wxPython==4.0.3
  Downloading https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-18.04/wxPython-4.0.3-cp36-cp36m-linux_x86_64.whl (121.7 MB)
Collecting opencv-python==3.4.5.20
  Using cached opencv_python-3.4.5.20-cp36-cp36m-manylinux1_x86_64.whl (25.4 MB)
Collecting deeplabcut
  Downloading deeplabcut-2.1.10.2-py3-none-any.whl (694 kB)
Collecting matplotlib==3.0.3
  Using cached matplotlib-3.0.3-cp36-cp36m-manylinux1_x86_64.whl (13.0 MB)
Collecting tables==3.4.3
  Downloading tables-3.4.3-cp36-cp36m-manylinux1_x86_64.whl (3.8 MB)
Collecting tensorflow-gpu==1.13.1
  Downloading tensorflow_gpu-1.13.1-cp36-cp36m-manylinux1_x86_64.whl (345.2 MB)
Collecting imgaug
  Using cached imgaug-0.4.0-py2.py3-none-any.whl (948 kB)
Collecting six
  Downloading six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting PyPubSub
  Using cached Pypubsub-4.0.3-py3-none-any.whl (61 kB)
Collecting numpy>=1.10.0
  Downloading numpy-1.19.5-cp36-cp36m-manylinux2010_x86_64.whl (14.8 MB)
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.3.1-cp36-cp36m-manylinux1_x86_64.whl (1.1 MB)
Collecting cycler>=0.10
  Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting python-dateutil>=2.1
  Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
  Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting numexpr>=2.5.2
  Downloading numexpr-2.7.2-cp36-cp36m-manylinux2010_x86_64.whl (469 kB)
Collecting tensorboard<1.14.0,>=1.13.0
  Using cached tensorboard-1.13.1-py3-none-any.whl (3.2 MB)
Collecting keras-applications>=1.0.6
  Downloading Keras_Applications-1.0.8-py3-none-any.whl (50 kB)
Collecting protobuf>=3.6.1
  Downloading protobuf-3.15.0-cp36-cp36m-manylinux1_x86_64.whl (1.0 MB)
Collecting gast>=0.2.0
  Downloading gast-0.4.0-py3-none-any.whl (9.8 kB)
Collecting absl-py>=0.1.6
  Downloading absl_py-0.11.0-py3-none-any.whl (127 kB)
Collecting astor>=0.6.0
  Downloading astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting tensorflow-estimator<1.14.0rc0,>=1.13.0
  Using cached tensorflow_estimator-1.13.0-py2.py3-none-any.whl (367 kB)
Requirement already satisfied: wheel>=0.26 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from tensorflow-gpu==1.13.1->-r /home/weertman/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/conda-environments/condaenv.izm11_wo.requirements.txt (line 5)) (0.36.2)
Collecting termcolor>=1.1.0
  Using cached termcolor-1.1.0.tar.gz (3.9 kB)
Collecting keras-preprocessing>=1.0.5
  Downloading Keras_Preprocessing-1.1.2-py2.py3-none-any.whl (42 kB)
Collecting grpcio>=1.8.6
  Downloading grpcio-1.35.0-cp36-cp36m-manylinux2014_x86_64.whl (4.1 MB)
Collecting h5py
  Downloading h5py-3.1.0-cp36-cp36m-manylinux1_x86_64.whl (4.0 MB)
Collecting werkzeug>=0.11.15
  Downloading Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB)
Collecting markdown>=2.6.8
  Downloading Markdown-3.3.3-py3-none-any.whl (96 kB)
Collecting importlib-metadata
  Downloading importlib_metadata-3.4.0-py3-none-any.whl (10 kB)
Collecting mock>=2.0.0
  Downloading mock-4.0.3-py3-none-any.whl (28 kB)
Collecting scikit-learn
  Downloading scikit_learn-0.24.1-cp36-cp36m-manylinux2010_x86_64.whl (22.2 MB)
Collecting chardet
  Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB)
Collecting click
  Using cached click-7.1.2-py2.py3-none-any.whl (82 kB)
Collecting tensorpack==0.9.8
  Downloading tensorpack-0.9.8-py2.py3-none-any.whl (288 kB)
Collecting deeplabcut
  Downloading deeplabcut-2.1.10.1-py3-none-any.whl (695 kB)
  Downloading deeplabcut-2.1.10-py3-none-any.whl (684 kB)
  Downloading deeplabcut-2.1.9-py3-none-any.whl (665 kB)
  Using cached deeplabcut-2.1.8.2-py3-none-any.whl (400 kB)
Collecting pyyaml>=5.1
  Downloading PyYAML-5.4.1-cp36-cp36m-manylinux1_x86_64.whl (640 kB)
Collecting scipy
  Downloading scipy-1.5.4-cp36-cp36m-manylinux1_x86_64.whl (25.9 MB)
Collecting tqdm
  Downloading tqdm-4.57.0-py2.py3-none-any.whl (72 kB)
Collecting numpy>=1.10.0
  Downloading numpy-1.16.4-cp36-cp36m-manylinux1_x86_64.whl (17.3 MB)
Collecting tensorpack>=0.9.7.1
  Downloading tensorpack-0.11-py2.py3-none-any.whl (296 kB)
Collecting patsy
  Using cached patsy-0.5.1-py2.py3-none-any.whl (231 kB)
Requirement already satisfied: certifi in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut->-r /home/weertman/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/conda-environments/condaenv.izm11_wo.requirements.txt (line 2)) (2020.12.5)
Collecting scikit-image
  Downloading scikit_image-0.17.2-cp36-cp36m-manylinux1_x86_64.whl (12.4 MB)
Collecting ipython
  Downloading ipython-7.16.1-py3-none-any.whl (785 kB)
Requirement already satisfied: setuptools in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut->-r /home/weertman/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/conda-environments/condaenv.izm11_wo.requirements.txt (line 2)) (52.0.0.post20210125)
Collecting ruamel.yaml~=0.15
  Downloading ruamel.yaml-0.16.12-py2.py3-none-any.whl (111 kB)
Collecting h5py
  Downloading h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9 MB)
Collecting requests
  Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB)
Collecting pandas>=1.0.
  Downloading pandas-1.1.5-cp36-cp36m-manylinux1_x86_64.whl (9.5 MB)
Collecting moviepy<=1.0.1
  Using cached moviepy-1.0.1.tar.gz (373 kB)
Collecting ipython-genutils
  Using cached ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)
Collecting statsmodels
  Downloading statsmodels-0.12.2-cp36-cp36m-manylinux1_x86_64.whl (9.5 MB)
Collecting intel-openmp
  Downloading intel_openmp-2021.1.2-py2.py3-none-manylinux1_x86_64.whl (1.9 MB)
Collecting easydict
  Using cached easydict-1.9.tar.gz (6.4 kB)
Collecting decorator<5.0,>=4.0.2
  Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting proglog<=1.0.0
  Using cached proglog-0.1.9.tar.gz (10 kB)
Collecting imageio<3.0,>=2.5
  Downloading imageio-2.9.0-py3-none-any.whl (3.3 MB)
Collecting imageio_ffmpeg>=0.2.0
  Downloading imageio_ffmpeg-0.4.3-py3-none-manylinux2010_x86_64.whl (26.9 MB)
Collecting pillow
  Downloading Pillow-8.1.0-cp36-cp36m-manylinux1_x86_64.whl (2.2 MB)
Collecting pytz>=2017.2
  Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB)
Collecting idna<3,>=2.5
  Using cached idna-2.10-py2.py3-none-any.whl (58 kB)
Collecting urllib3<1.27,>=1.21.1
  Downloading urllib3-1.26.3-py2.py3-none-any.whl (137 kB)
Collecting ruamel.yaml.clib>=0.1.2
  Downloading ruamel.yaml.clib-0.2.2-cp36-cp36m-manylinux1_x86_64.whl (549 kB)
Collecting msgpack>=0.5.2
  Downloading msgpack-1.0.2-cp36-cp36m-manylinux1_x86_64.whl (272 kB)
Collecting tabulate>=0.7.7
  Downloading tabulate-0.8.8-py3-none-any.whl (25 kB)
Collecting psutil>=5
  Downloading psutil-5.8.0-cp36-cp36m-manylinux2010_x86_64.whl (291 kB)
Collecting msgpack-numpy>=0.4.4.2
  Downloading msgpack_numpy-0.4.7.1-py2.py3-none-any.whl (6.7 kB)
Collecting pyzmq>=16
  Downloading pyzmq-22.0.3-cp36-cp36m-manylinux1_x86_64.whl (1.1 MB)
Collecting Shapely
  Downloading Shapely-1.7.1-cp36-cp36m-manylinux1_x86_64.whl (1.0 MB)
Collecting tifffile>=2019.7.26
  Downloading tifffile-2020.9.3-py3-none-any.whl (148 kB)
Collecting PyWavelets>=1.1.1
  Downloading PyWavelets-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (4.4 MB)
Collecting networkx>=2.0
  Downloading networkx-2.5-py3-none-any.whl (1.6 MB)
Collecting typing-extensions>=3.6.4
  Downloading typing_extensions-3.7.4.3-py3-none-any.whl (22 kB)
Collecting zipp>=0.5
  Downloading zipp-3.4.0-py3-none-any.whl (5.2 kB)
Collecting traitlets>=4.2
  Downloading traitlets-4.3.3-py2.py3-none-any.whl (75 kB)
Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0
  Downloading prompt_toolkit-3.0.16-py3-none-any.whl (366 kB)
Collecting jedi>=0.10
  Downloading jedi-0.18.0-py2.py3-none-any.whl (1.4 MB)
Collecting pygments
  Downloading Pygments-2.8.0-py3-none-any.whl (983 kB)
Collecting pickleshare
  Using cached pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Collecting backcall
  Downloading backcall-0.2.0-py2.py3-none-any.whl (11 kB)
Collecting pexpect
  Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
Collecting parso<0.9.0,>=0.8.0
  Downloading parso-0.8.1-py2.py3-none-any.whl (93 kB)
Collecting wcwidth
  Downloading wcwidth-0.2.5-py2.py3-none-any.whl (30 kB)
Collecting ptyprocess>=0.5
  Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB)
Collecting joblib>=0.11
  Downloading joblib-1.0.1-py3-none-any.whl (303 kB)
Collecting threadpoolctl>=2.0.0
  Using cached threadpoolctl-2.1.0-py3-none-any.whl (12 kB)
Building wheels for collected packages: termcolor, moviepy, proglog, easydict
  Building wheel for termcolor (setup.py): started
  Building wheel for termcolor (setup.py): finished with status 'done'
  Created wheel for termcolor: filename=termcolor-1.1.0-py3-none-any.whl size=4829 sha256=deca25c797a162fa2fcdbeca8ff2a143f3c8ac23af9729c16985cbce65479d37
  Stored in directory: /home/weertman/.cache/pip/wheels/93/2a/eb/e58dbcbc963549ee4f065ff80a59f274cc7210b6eab962acdc
  Building wheel for moviepy (setup.py): started
  Building wheel for moviepy (setup.py): finished with status 'done'
  Created wheel for moviepy: filename=moviepy-1.0.1-py3-none-any.whl size=110787 sha256=8a82ff2e2e11f468e62e98573c0d529cade87827a0aa6ecfc9bcaea124f4e0d9
  Stored in directory: /home/weertman/.cache/pip/wheels/bf/7d/8d/44323f01f0cc80ac445b8b707c4716458d7db58f00c6007830
  Building wheel for proglog (setup.py): started
  Building wheel for proglog (setup.py): finished with status 'done'
  Created wheel for proglog: filename=proglog-0.1.9-py3-none-any.whl size=6147 sha256=1bc5f4ad97983ec1e645265c854d103186eb998bd6df7f44e4f0f4c4d7bf2e65
  Stored in directory: /home/weertman/.cache/pip/wheels/e7/11/a0/7e65f734d33043735a557b1244569cca327353db9068158076
  Building wheel for easydict (setup.py): started
  Building wheel for easydict (setup.py): finished with status 'done'
  Created wheel for easydict: filename=easydict-1.9-py3-none-any.whl size=6350 sha256=f8c1a30ae4e7c8055d822c7bf4dc6b985e529d3e4742e65545829f7f46a5e588
  Stored in directory: /home/weertman/.cache/pip/wheels/5d/79/e4/4e55effe206295359b37e0f9db3e68a1197ba396682807dadb
Successfully built termcolor moviepy proglog easydict
Installing collected packages: six, zipp, typing-extensions, python-dateutil, pyparsing, pillow, numpy, kiwisolver, decorator, cycler, wcwidth, urllib3, tqdm, tifffile, scipy, PyWavelets, pytz, ptyprocess, parso, networkx, msgpack, matplotlib, ipython-genutils, importlib-metadata, imageio, idna, chardet, werkzeug, traitlets, threadpoolctl, termcolor, tabulate, Shapely, scikit-image, ruamel.yaml.clib, requests, pyzmq, pygments, psutil, protobuf, prompt-toolkit, proglog, pickleshare, pexpect, patsy, pandas, opencv-python, numexpr, msgpack-numpy, mock, markdown, joblib, jedi, imageio-ffmpeg, h5py, grpcio, backcall, absl-py, tensorpack, tensorflow-estimator, tensorboard, tables, statsmodels, scikit-learn, ruamel.yaml, pyyaml, PyPubSub, moviepy, keras-preprocessing, keras-applications, ipython, intel-openmp, imgaug, gast, easydict, click, astor, wxPython, tensorflow-gpu, deeplabcut
Successfully installed PyPubSub-4.0.3 PyWavelets-1.1.1 Shapely-1.7.1 absl-py-0.11.0 astor-0.8.1 backcall-0.2.0 chardet-4.0.0 click-7.1.2 cycler-0.10.0 decorator-4.4.2 deeplabcut-2.1.8.2 easydict-1.9 gast-0.4.0 grpcio-1.35.0 h5py-2.10.0 idna-2.10 imageio-2.9.0 imageio-ffmpeg-0.4.3 imgaug-0.4.0 importlib-metadata-3.4.0 intel-openmp-2021.1.2 ipython-7.16.1 ipython-genutils-0.2.0 jedi-0.18.0 joblib-1.0.1 keras-applications-1.0.8 keras-preprocessing-1.1.2 kiwisolver-1.3.1 markdown-3.3.3 matplotlib-3.0.3 mock-4.0.3 moviepy-1.0.1 msgpack-1.0.2 msgpack-numpy-0.4.7.1 networkx-2.5 numexpr-2.7.2 numpy-1.16.4 opencv-python-3.4.5.20 pandas-1.1.5 parso-0.8.1 patsy-0.5.1 pexpect-4.8.0 pickleshare-0.7.5 pillow-8.1.0 proglog-0.1.9 prompt-toolkit-3.0.16 protobuf-3.15.0 psutil-5.8.0 ptyprocess-0.7.0 pygments-2.8.0 pyparsing-2.4.7 python-dateutil-2.8.1 pytz-2021.1 pyyaml-5.4.1 pyzmq-22.0.3 requests-2.25.1 ruamel.yaml-0.16.12 ruamel.yaml.clib-0.2.2 scikit-image-0.17.2 scikit-learn-0.24.1 scipy-1.5.4 six-1.15.0 statsmodels-0.12.2 tables-3.4.3 tabulate-0.8.8 tensorboard-1.13.1 tensorflow-estimator-1.13.0 tensorflow-gpu-1.13.1 tensorpack-0.11 termcolor-1.1.0 threadpoolctl-2.1.0 tifffile-2020.9.3 tqdm-4.57.0 traitlets-4.3.3 typing-extensions-3.7.4.3 urllib3-1.26.3 wcwidth-0.2.5 werkzeug-1.0.1 wxPython-4.0.3 zipp-3.4.0

#
# To activate this environment, use
#
#     $ conda activate dgp
#
# To deactivate an active environment, use
#
#     $ conda deactivate
(base) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/conda-environments$ source activate dgp
(dgp) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/conda-environments$ cd ../
(dgp) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut$ pip install -e

Usage:   
  pip install [options] <requirement specifier> [package-index-options] ...
  pip install [options] -r <requirements file> [package-index-options] ...
  pip install [options] [-e] <vcs project url> ...
  pip install [options] [-e] <local project path> ...
  pip install [options] <archive url/path> ...

-e option requires 1 argument
(dgp) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut$ pip install -e .
Obtaining file:///home/weertman/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut
Requirement already satisfied: certifi in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (2020.12.5)
Requirement already satisfied: chardet in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (4.0.0)
Requirement already satisfied: click in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (7.1.2)
Requirement already satisfied: easydict in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (1.9)
Requirement already satisfied: h5py~=2.7 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (2.10.0)
Requirement already satisfied: intel-openmp in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (2021.1.2)
Requirement already satisfied: imgaug in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (0.4.0)
Requirement already satisfied: ipython in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (7.16.1)
Requirement already satisfied: ipython-genutils in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (0.2.0)
Requirement already satisfied: matplotlib==3.0.3 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (3.0.3)
Requirement already satisfied: moviepy in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (1.0.1)
Requirement already satisfied: numpy>=1.16.4 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (1.16.4)
Requirement already satisfied: opencv-python~=3.4 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (3.4.5.20)
Requirement already satisfied: pandas in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (1.1.5)
Requirement already satisfied: patsy in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (0.5.1)
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Requirement already satisfied: requests in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (2.25.1)
Requirement already satisfied: ruamel.yaml~=0.15 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (0.16.12)
Requirement already satisfied: setuptools in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (52.0.0.post20210125)
Requirement already satisfied: scikit-image in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (0.17.2)
Requirement already satisfied: scikit-learn in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (0.24.1)
Requirement already satisfied: scipy in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (1.5.4)
Requirement already satisfied: six in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (1.15.0)
Collecting statsmodels==0.10.1
  Downloading statsmodels-0.10.1-cp36-cp36m-manylinux1_x86_64.whl (8.1 MB)
     |████████████████████████████████| 8.1 MB 4.7 MB/s 
Requirement already satisfied: tables==3.4.3 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (3.4.3)
Requirement already satisfied: tensorpack>=0.9.7.1 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (0.11)
Requirement already satisfied: tqdm in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (4.57.0)
Requirement already satisfied: wheel in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (0.36.2)
Requirement already satisfied: cycler>=0.10 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from matplotlib==3.0.3->deeplabcut==2.1.4) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from matplotlib==3.0.3->deeplabcut==2.1.4) (1.3.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from matplotlib==3.0.3->deeplabcut==2.1.4) (2.4.7)
Requirement already satisfied: numexpr>=2.5.2 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from tables==3.4.3->deeplabcut==2.1.4) (2.7.2)
Requirement already satisfied: pytz>=2017.2 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from pandas->deeplabcut==2.1.4) (2021.1)
Requirement already satisfied: ruamel.yaml.clib>=0.1.2 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from ruamel.yaml~=0.15->deeplabcut==2.1.4) (0.2.2)
Requirement already satisfied: pyzmq>=16 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from tensorpack>=0.9.7.1->deeplabcut==2.1.4) (22.0.3)
Requirement already satisfied: psutil>=5 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from tensorpack>=0.9.7.1->deeplabcut==2.1.4) (5.8.0)
Requirement already satisfied: msgpack>=0.5.2 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from tensorpack>=0.9.7.1->deeplabcut==2.1.4) (1.0.2)
Requirement already satisfied: tabulate>=0.7.7 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from tensorpack>=0.9.7.1->deeplabcut==2.1.4) (0.8.8)
Requirement already satisfied: msgpack-numpy>=0.4.4.2 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from tensorpack>=0.9.7.1->deeplabcut==2.1.4) (0.4.7.1)
Requirement already satisfied: termcolor>=1.1 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from tensorpack>=0.9.7.1->deeplabcut==2.1.4) (1.1.0)
Requirement already satisfied: Pillow in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from imgaug->deeplabcut==2.1.4) (8.1.0)
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Requirement already satisfied: Shapely in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from imgaug->deeplabcut==2.1.4) (1.7.1)
Requirement already satisfied: tifffile>=2019.7.26 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from scikit-image->deeplabcut==2.1.4) (2020.9.3)
Requirement already satisfied: networkx>=2.0 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from scikit-image->deeplabcut==2.1.4) (2.5)
Requirement already satisfied: PyWavelets>=1.1.1 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from scikit-image->deeplabcut==2.1.4) (1.1.1)
Requirement already satisfied: decorator>=4.3.0 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from networkx>=2.0->scikit-image->deeplabcut==2.1.4) (4.4.2)
Requirement already satisfied: backcall in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from ipython->deeplabcut==2.1.4) (0.2.0)
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Requirement already satisfied: pexpect in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from ipython->deeplabcut==2.1.4) (4.8.0)
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Requirement already satisfied: wcwidth in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->deeplabcut==2.1.4) (0.2.5)
Requirement already satisfied: proglog<=1.0.0 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from moviepy->deeplabcut==2.1.4) (0.1.9)
Requirement already satisfied: imageio-ffmpeg>=0.2.0 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from moviepy->deeplabcut==2.1.4) (0.4.3)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from requests->deeplabcut==2.1.4) (1.26.3)
Requirement already satisfied: idna<3,>=2.5 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from requests->deeplabcut==2.1.4) (2.10)
Requirement already satisfied: ptyprocess>=0.5 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from pexpect->ipython->deeplabcut==2.1.4) (0.7.0)
Requirement already satisfied: threadpoolctl>=2.0.0 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from scikit-learn->deeplabcut==2.1.4) (2.1.0)
Requirement already satisfied: joblib>=0.11 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from scikit-learn->deeplabcut==2.1.4) (1.0.1)
Installing collected packages: statsmodels, deeplabcut
  Attempting uninstall: statsmodels
    Found existing installation: statsmodels 0.12.2
    Uninstalling statsmodels-0.12.2:
      Successfully uninstalled statsmodels-0.12.2
  Attempting uninstall: deeplabcut
    Found existing installation: deeplabcut 2.1.8.2
    Uninstalling deeplabcut-2.1.8.2:
      Successfully uninstalled deeplabcut-2.1.8.2
  Running setup.py develop for deeplabcut
Successfully installed deeplabcut statsmodels-0.10.1
(dgp) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut$ cd ../..
(dgp) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose$ pip install -e .
Obtaining file:///home/weertman/Documents/DGP_MODELS/deepgraphpose
Installing collected packages: deepgraphpose
  Running setup.py develop for deepgraphpose
Successfully installed deepgraphpose
(dgp) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose$ conda install -c anaconda wxpython
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.9.2

Please update conda by running

    $ conda update -n base -c defaults conda

## Package Plan ##

  environment location: /home/weertman/anaconda3/envs/dgp

  added / updated specs:
    - wxpython

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2020.10.14 |                0         128 KB  anaconda
    cairo-1.14.12              |       h8948797_3         1.3 MB  anaconda
    certifi-2020.6.20          |           py36_0         160 KB  anaconda
    expat-2.2.10               |       he6710b0_2         192 KB  anaconda
    fontconfig-2.13.0          |       h9420a91_0         291 KB  anaconda
    freetype-2.10.4            |       h5ab3b9f_0         901 KB  anaconda
    fribidi-1.0.10             |       h7b6447c_0         115 KB  anaconda
    gettext-0.19.8.1           |       h9b4dc7a_1         3.7 MB  anaconda
    graphite2-1.3.14           |       h23475e2_0         102 KB  anaconda
    gst-plugins-base-1.14.0    |       hbbd80ab_1         6.3 MB  anaconda
    gstreamer-1.14.0           |       hb453b48_1         3.8 MB  anaconda
    icu-58.2                   |       he6710b0_3        22.7 MB  anaconda
    libglu-9.0.0               |       hf484d3e_1         377 KB  anaconda
    libpng-1.6.37              |       hbc83047_0         364 KB  anaconda
    libuuid-1.0.3              |       h1bed415_2          16 KB  anaconda
    libxcb-1.14                |       h7b6447c_0         610 KB  anaconda
    libxml2-2.9.10             |       hb55368b_3         1.3 MB  anaconda
    openssl-1.1.1h             |       h7b6447c_0         3.8 MB  anaconda
    pango-1.42.4               |       h049681c_0         528 KB  anaconda
    pcre-8.44                  |       he6710b0_0         269 KB  anaconda
    pixman-0.40.0              |       h7b6447c_0         628 KB  anaconda
    six-1.15.0                 |             py_0          13 KB  anaconda
    wxpython-4.0.4             |   py36hc99224d_0        20.0 MB  anaconda
    ------------------------------------------------------------
                                           Total:        67.5 MB

The following NEW packages will be INSTALLED:

  cairo              anaconda/linux-64::cairo-1.14.12-h8948797_3
  expat              anaconda/linux-64::expat-2.2.10-he6710b0_2
  fontconfig         anaconda/linux-64::fontconfig-2.13.0-h9420a91_0
  freetype           anaconda/linux-64::freetype-2.10.4-h5ab3b9f_0
  fribidi            anaconda/linux-64::fribidi-1.0.10-h7b6447c_0
  gettext            anaconda/linux-64::gettext-0.19.8.1-h9b4dc7a_1
  glib               anaconda/linux-64::glib-2.56.2-hd408876_0
  graphite2          anaconda/linux-64::graphite2-1.3.14-h23475e2_0
  gst-plugins-base   anaconda/linux-64::gst-plugins-base-1.14.0-hbbd80ab_1
  gstreamer          anaconda/linux-64::gstreamer-1.14.0-hb453b48_1
  harfbuzz           anaconda/linux-64::harfbuzz-1.8.8-hffaf4a1_0
  icu                anaconda/linux-64::icu-58.2-he6710b0_3
  jpeg               anaconda/linux-64::jpeg-9b-habf39ab_1
  libglu             anaconda/linux-64::libglu-9.0.0-hf484d3e_1
  libpng             anaconda/linux-64::libpng-1.6.37-hbc83047_0
  libuuid            anaconda/linux-64::libuuid-1.0.3-h1bed415_2
  libxcb             anaconda/linux-64::libxcb-1.14-h7b6447c_0
  libxml2            anaconda/linux-64::libxml2-2.9.10-hb55368b_3
  pango              anaconda/linux-64::pango-1.42.4-h049681c_0
  pcre               anaconda/linux-64::pcre-8.44-he6710b0_0
  pixman             anaconda/linux-64::pixman-0.40.0-h7b6447c_0
  six                anaconda/noarch::six-1.15.0-py_0
  wxpython           anaconda/linux-64::wxpython-4.0.4-py36hc99224d_0

The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    pkgs/main::ca-certificates-2021.1.19-~ --> anaconda::ca-certificates-2020.10.14-0
  certifi            pkgs/main::certifi-2020.12.5-py36h06a~ --> anaconda::certifi-2020.6.20-py36_0
  openssl              pkgs/main::openssl-1.1.1j-h27cfd23_0 --> anaconda::openssl-1.1.1h-h7b6447c_0

Proceed ([y]/n)? y

Downloading and Extracting Packages
gst-plugins-base-1.1 | 6.3 MB    | ################################################################## | 100% 
certifi-2020.6.20    | 160 KB    | ################################################################## | 100% 
fribidi-1.0.10       | 115 KB    | ################################################################## | 100% 
graphite2-1.3.14     | 102 KB    | ################################################################## | 100% 
pango-1.42.4         | 528 KB    | ################################################################## | 100% 
cairo-1.14.12        | 1.3 MB    | ################################################################## | 100% 
libxml2-2.9.10       | 1.3 MB    | ################################################################## | 100% 
expat-2.2.10         | 192 KB    | ################################################################## | 100% 
gstreamer-1.14.0     | 3.8 MB    | ################################################################## | 100% 
pixman-0.40.0        | 628 KB    | ################################################################## | 100% 
six-1.15.0           | 13 KB     | ################################################################## | 100% 
libpng-1.6.37        | 364 KB    | ################################################################## | 100% 
gettext-0.19.8.1     | 3.7 MB    | ################################################################## | 100% 
libxcb-1.14          | 610 KB    | ################################################################## | 100% 
wxpython-4.0.4       | 20.0 MB   | ################################################################## | 100% 
freetype-2.10.4      | 901 KB    | ################################################################## | 100% 
fontconfig-2.13.0    | 291 KB    | ################################################################## | 100% 
libglu-9.0.0         | 377 KB    | ################################################################## | 100% 
pcre-8.44            | 269 KB    | ################################################################## | 100% 
libuuid-1.0.3        | 16 KB     | ################################################################## | 100% 
openssl-1.1.1h       | 3.8 MB    | ################################################################## | 100% 
icu-58.2             | 22.7 MB   | ################################################################## | 100% 
ca-certificates-2020 | 128 KB    | ################################################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(dgp) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose$ ipython
Python 3.6.8 |Anaconda, Inc.| (default, Dec 30 2018, 01:22:34) 
Type 'copyright', 'credits' or 'license' for more information
IPython 7.16.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import deeplabcut
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
~/anaconda3/envs/dgp/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py in <module>
     57 
---> 58   from tensorflow.python.pywrap_tensorflow_internal import *
     59   from tensorflow.python.pywrap_tensorflow_internal import __version__

~/anaconda3/envs/dgp/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py in <module>
     27             return _mod
---> 28     _pywrap_tensorflow_internal = swig_import_helper()
     29     del swig_import_helper

~/anaconda3/envs/dgp/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py in swig_import_helper()
     23             try:
---> 24                 _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
     25             finally:

~/anaconda3/envs/dgp/lib/python3.6/imp.py in load_module(name, file, filename, details)
    242         else:
--> 243             return load_dynamic(name, filename, file)
    244     elif type_ == PKG_DIRECTORY:

~/anaconda3/envs/dgp/lib/python3.6/imp.py in load_dynamic(name, path, file)
    342             name=name, loader=loader, origin=path)
--> 343         return _load(spec)
    344 

ImportError: libcublas.so.10.0: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

ImportError                               Traceback (most recent call last)
<ipython-input-1-cfa4f159dfc5> in <module>
----> 1 import deeplabcut

~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/deeplabcut/__init__.py in <module>
     28     else:
     29         mpl.use('Agg')
---> 30     from deeplabcut import generate_training_dataset
     31     from deeplabcut import refine_training_dataset
     32     from deeplabcut.generate_training_dataset import label_frames, dropannotationfileentriesduetodeletedimages, comparevideolistsanddatafolders, dropimagesduetolackofannotation

~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/deeplabcut/generate_training_dataset/__init__.py in <module>
     17 else:
     18     from deeplabcut.generate_training_dataset.auxfun_drag_label import *
---> 19     from deeplabcut.generate_training_dataset.labeling_toolbox import *
     20     from deeplabcut.generate_training_dataset.multiple_individual_labeling_toolbox import *
     21     from deeplabcut.generate_training_dataset.frame_extraction_toolbox import *

~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/deeplabcut/generate_training_dataset/labeling_toolbox.py in <module>
     25 import argparse
     26 from deeplabcut.generate_training_dataset import auxfun_drag_label
---> 27 from deeplabcut.utils import auxiliaryfunctions
     28 from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
     29 from matplotlib.backends.backend_wxagg import NavigationToolbar2WxAgg as NavigationToolbar

~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/deeplabcut/utils/__init__.py in <module>
----> 1 from deeplabcut.utils.make_labeled_video import *
      2 from deeplabcut.utils.auxiliaryfunctions import *
      3 from deeplabcut.utils.video_processor import *
      4 from deeplabcut.utils.plotting import *
      5 

~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/deeplabcut/utils/make_labeled_video.py in <module>
     36 
     37 from deeplabcut.utils import auxiliaryfunctions
---> 38 from deeplabcut.pose_estimation_tensorflow.config import load_config
     39 from skimage.util import img_as_ubyte
     40 from skimage.draw import circle_perimeter, circle, line,line_aa

~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/deeplabcut/pose_estimation_tensorflow/__init__.py in <module>
     11 from deeplabcut.pose_estimation_tensorflow.dataset import *
     12 from deeplabcut.pose_estimation_tensorflow.models import *
---> 13 from deeplabcut.pose_estimation_tensorflow.nnet import *
     14 from deeplabcut.pose_estimation_tensorflow.util import *
     15 

~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/deeplabcut/pose_estimation_tensorflow/nnet/__init__.py in <module>
     12 
     13 """
---> 14 from deeplabcut.pose_estimation_tensorflow.nnet.losses import *
     15 from deeplabcut.pose_estimation_tensorflow.nnet.net_factory import *
     16 from deeplabcut.pose_estimation_tensorflow.nnet.pose_net import *

~/Documents/DGP_MODELS/deepgraphpose/src/DeepLabCut/deeplabcut/pose_estimation_tensorflow/nnet/losses.py in <module>
      3 https://github.com/eldar/pose-tensorflow
      4 '''
----> 5 import tensorflow as tf
      6 vers = (tf.__version__).split('.')
      7 if int(vers[0])==1 and int(vers[1])>12:

~/anaconda3/envs/dgp/lib/python3.6/site-packages/tensorflow/__init__.py in <module>
     22 
     23 # pylint: disable=g-bad-import-order
---> 24 from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
     25 
     26 from tensorflow._api.v1 import app

~/anaconda3/envs/dgp/lib/python3.6/site-packages/tensorflow/python/__init__.py in <module>
     47 import numpy as np
     48 
---> 49 from tensorflow.python import pywrap_tensorflow
     50 
     51 # Protocol buffers

~/anaconda3/envs/dgp/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py in <module>
     72 for some common reasons and solutions.  Include the entire stack trace
     73 above this error message when asking for help.""" % traceback.format_exc()
---> 74   raise ImportError(msg)
     75 
     76 # pylint: enable=wildcard-import,g-import-not-at-top,unused-import,line-too-long

ImportError: Traceback (most recent call last):
  File "/home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
    from tensorflow.python.pywrap_tensorflow_internal import *
  File "/home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
    _pywrap_tensorflow_internal = swig_import_helper()
  File "/home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
    _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
  File "/home/weertman/anaconda3/envs/dgp/lib/python3.6/imp.py", line 243, in load_module
    return load_dynamic(name, filename, file)
  File "/home/weertman/anaconda3/envs/dgp/lib/python3.6/imp.py", line 343, in load_dynamic
    return _load(spec)
ImportError: libcublas.so.10.0: cannot open shared object file: No such file or directory

Failed to load the native TensorFlow runtime.

See https://www.tensorflow.org/install/errors

for some common reasons and solutions.  Include the entire stack trace
above this error message when asking for help.

In [2]: import deepgraphpose

went ahead and checked what libraries were installed in the environment

(dgp) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose$ conda list
# packages in environment at /home/weertman/anaconda3/envs/dgp:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
absl-py                   0.11.0                   pypi_0    pypi
astor                     0.8.1                    pypi_0    pypi
backcall                  0.2.0                    pypi_0    pypi
ca-certificates           2020.10.14                    0    anaconda
cairo                     1.14.12              h8948797_3    anaconda
certifi                   2020.6.20                py36_0    anaconda
chardet                   4.0.0                    pypi_0    pypi
click                     7.1.2                    pypi_0    pypi
cycler                    0.10.0                   pypi_0    pypi
decorator                 4.4.2                    pypi_0    pypi
deepgraphpose             0.1.0                     dev_0    <develop>
deeplabcut                2.1.4                     dev_0    <develop>
easydict                  1.9                      pypi_0    pypi
expat                     2.2.10               he6710b0_2    anaconda
fontconfig                2.13.0               h9420a91_0    anaconda
freetype                  2.10.4               h5ab3b9f_0    anaconda
fribidi                   1.0.10               h7b6447c_0    anaconda
gast                      0.4.0                    pypi_0    pypi
gettext                   0.19.8.1             h9b4dc7a_1    anaconda
glib                      2.56.2               hd408876_0    anaconda
graphite2                 1.3.14               h23475e2_0    anaconda
grpcio                    1.35.0                   pypi_0    pypi
gst-plugins-base          1.14.0               hbbd80ab_1    anaconda
gstreamer                 1.14.0               hb453b48_1    anaconda
h5py                      2.10.0                   pypi_0    pypi
harfbuzz                  1.8.8                hffaf4a1_0    anaconda
icu                       58.2                 he6710b0_3    anaconda
idna                      2.10                     pypi_0    pypi
imageio                   2.9.0                    pypi_0    pypi
imageio-ffmpeg            0.4.3                    pypi_0    pypi
imgaug                    0.4.0                    pypi_0    pypi
importlib-metadata        3.4.0                    pypi_0    pypi
intel-openmp              2021.1.2                 pypi_0    pypi
ipython                   7.16.1                   pypi_0    pypi
ipython-genutils          0.2.0                    pypi_0    pypi
jedi                      0.18.0                   pypi_0    pypi
joblib                    1.0.1                    pypi_0    pypi
jpeg                      9b                   habf39ab_1    anaconda
keras-applications        1.0.8                    pypi_0    pypi
keras-preprocessing       1.1.2                    pypi_0    pypi
kiwisolver                1.3.1                    pypi_0    pypi
libedit                   3.1.20191231         h14c3975_1  
libffi                    3.2.1             hf484d3e_1007  
libgcc-ng                 9.1.0                hdf63c60_0  
libglu                    9.0.0                hf484d3e_1    anaconda
libpng                    1.6.37               hbc83047_0    anaconda
libstdcxx-ng              9.1.0                hdf63c60_0  
libuuid                   1.0.3                h1bed415_2    anaconda
libxcb                    1.14                 h7b6447c_0    anaconda
libxml2                   2.9.10               hb55368b_3    anaconda
markdown                  3.3.3                    pypi_0    pypi
matplotlib                3.0.3                    pypi_0    pypi
mock                      4.0.3                    pypi_0    pypi
moviepy                   1.0.1                    pypi_0    pypi
msgpack                   1.0.2                    pypi_0    pypi
msgpack-numpy             0.4.7.1                  pypi_0    pypi
ncurses                   6.2                  he6710b0_1  
networkx                  2.5                      pypi_0    pypi
numexpr                   2.7.2                    pypi_0    pypi
numpy                     1.16.4                   pypi_0    pypi
opencv-python             3.4.5.20                 pypi_0    pypi
openssl                   1.1.1h               h7b6447c_0    anaconda
pandas                    1.1.5                    pypi_0    pypi
pango                     1.42.4               h049681c_0    anaconda
parso                     0.8.1                    pypi_0    pypi
patsy                     0.5.1                    pypi_0    pypi
pcre                      8.44                 he6710b0_0    anaconda
pexpect                   4.8.0                    pypi_0    pypi
pickleshare               0.7.5                    pypi_0    pypi
pillow                    8.1.0                    pypi_0    pypi
pip                       21.0.1           py36h06a4308_0  
pixman                    0.40.0               h7b6447c_0    anaconda
proglog                   0.1.9                    pypi_0    pypi
prompt-toolkit            3.0.16                   pypi_0    pypi
protobuf                  3.15.0                   pypi_0    pypi
psutil                    5.8.0                    pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
pygments                  2.8.0                    pypi_0    pypi
pyparsing                 2.4.7                    pypi_0    pypi
pypubsub                  4.0.3                    pypi_0    pypi
python                    3.6.8                h0371630_0  
python-dateutil           2.8.1                    pypi_0    pypi
pytz                      2021.1                   pypi_0    pypi
pywavelets                1.1.1                    pypi_0    pypi
pyyaml                    5.4.1                    pypi_0    pypi
pyzmq                     22.0.3                   pypi_0    pypi
readline                  7.0                  h7b6447c_5  
requests                  2.25.1                   pypi_0    pypi
ruamel-yaml               0.16.12                  pypi_0    pypi
ruamel-yaml-clib          0.2.2                    pypi_0    pypi
scikit-image              0.17.2                   pypi_0    pypi
scikit-learn              0.24.1                   pypi_0    pypi
scipy                     1.5.4                    pypi_0    pypi
setuptools                52.0.0           py36h06a4308_0  
shapely                   1.7.1                    pypi_0    pypi
six                       1.15.0                     py_0    anaconda
sqlite                    3.33.0               h62c20be_0  
statsmodels               0.10.1                   pypi_0    pypi
tables                    3.4.3                    pypi_0    pypi
tabulate                  0.8.8                    pypi_0    pypi
tensorboard               1.13.1                   pypi_0    pypi
tensorflow-estimator      1.13.0                   pypi_0    pypi
tensorflow-gpu            1.13.1                   pypi_0    pypi
tensorpack                0.11                     pypi_0    pypi
termcolor                 1.1.0                    pypi_0    pypi
threadpoolctl             2.1.0                    pypi_0    pypi
tifffile                  2020.9.3                 pypi_0    pypi
tk                        8.6.10               hbc83047_0  
tqdm                      4.57.0                   pypi_0    pypi
traitlets                 4.3.3                    pypi_0    pypi
typing-extensions         3.7.4.3                  pypi_0    pypi
urllib3                   1.26.3                   pypi_0    pypi
wcwidth                   0.2.5                    pypi_0    pypi
werkzeug                  1.0.1                    pypi_0    pypi
wheel                     0.36.2             pyhd3eb1b0_0  
wxpython                  4.0.3                    pypi_0    pypi
xz                        5.2.5                h7b6447c_0  
zipp                      3.4.0                    pypi_0    pypi
zlib                      1.2.11               h7b6447c_3

looks like tensorflow and tensorflow-base are missing in the install to the conda environment from the yaml. should I manually install these?

wweertman commented 3 years ago

conda version is not the issue. updated and re-ran it all

wweertman commented 3 years ago

(dgp) weertman@weertman-Z270P-D3:~/Documents/DGP_MODELS/deepgraphpose$ curl http://download.tensorflow.org/models/resnet_v1_50_2016_08_28.tar.gz | tar xvz -C src/DeepLabCut/deeplabcut/pose_estimation_tensorflow/models/pretrained/
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0resnet_v1_50.ckpt
100 90.6M  100 90.6M    0     0   9.7M      0  0:00:09  0:00:09 --:--:-- 10.1M

no issue downloading the pre-trained values. issue i had before was a windows thing it think.

wweertman commented 3 years ago

deeplabcut works fine in the DLC-GPU environment installed by the DLC-GPU.yaml from deeplabcut

wweertman commented 3 years ago

seems to be working now on windows. I am closing this.

paninski-lab / deepgraphpose

Questions #5