Closed wweertman closed 3 years ago
Is there a way to incorporate already labelled dataset into your workflow and start training from a snapshot?
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.
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
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.
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/".
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
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.
Could you share your config.yaml?
In your config.yaml:
TrainingFraction:
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:
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) ]]
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.
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.
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
(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?
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.
(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.
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'
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.
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
The same issue, the path format is written for Linux by default.
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?
Yeah, thanks for your patience to go through these errors. This provides us a lot of useful feedbacks.
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
Change videos/reachingvideo1.avi into windows format in the code?
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
Interesting, can you print out yaml_cfg[‘video_set’] and see what happens?
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'}}
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'```
Then maybe use this full path starting from C:
The default working path should be in Reaching-xxx, that’s why we can use the relative path. It would be worth checking that.
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
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
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.
(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
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
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.
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.
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.
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
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
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.
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.
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'
(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)
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Downloading tables-3.4.3-cp36-cp36m-manylinux1_x86_64.whl (3.8 MB)
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Downloading tensorflow_gpu-1.13.1-cp36-cp36m-manylinux1_x86_64.whl (345.2 MB)
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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)
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Using cached click-7.1.2-py2.py3-none-any.whl (82 kB)
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Downloading tensorpack-0.9.8-py2.py3-none-any.whl (288 kB)
Collecting deeplabcut
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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)
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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)
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Building wheels for collected packages: termcolor, moviepy, proglog, easydict
Building wheel for termcolor (setup.py): started
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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
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Stored in directory: /home/weertman/.cache/pip/wheels/bf/7d/8d/44323f01f0cc80ac445b8b707c4716458d7db58f00c6007830
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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
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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)
Requirement already satisfied: python-dateutil in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (2.8.1)
Requirement already satisfied: pyyaml>=5.1 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from deeplabcut==2.1.4) (5.4.1)
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)
Requirement already satisfied: imageio in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from imgaug->deeplabcut==2.1.4) (2.9.0)
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)
Requirement already satisfied: jedi>=0.10 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from ipython->deeplabcut==2.1.4) (0.18.0)
Requirement already satisfied: pygments in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from ipython->deeplabcut==2.1.4) (2.8.0)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from ipython->deeplabcut==2.1.4) (3.0.16)
Requirement already satisfied: pexpect in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from ipython->deeplabcut==2.1.4) (4.8.0)
Requirement already satisfied: pickleshare in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from ipython->deeplabcut==2.1.4) (0.7.5)
Requirement already satisfied: traitlets>=4.2 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from ipython->deeplabcut==2.1.4) (4.3.3)
Requirement already satisfied: parso<0.9.0,>=0.8.0 in /home/weertman/anaconda3/envs/dgp/lib/python3.6/site-packages (from jedi>=0.10->ipython->deeplabcut==2.1.4) (0.8.1)
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?
conda version is not the issue. updated and re-ran it all
(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.
deeplabcut works fine in the DLC-GPU environment installed by the DLC-GPU.yaml from deeplabcut
seems to be working now on windows. I am closing this.
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?