error during video compression #71
Comments
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Try downgrading to opencv 3. The bug is fixed in the current HEAD in the
repo but I haven't updated it in the conda-forge version.
…On Thursday, January 16, 2020, cooketho ***@***.***> wrote:
I'm getting the following error when I use Tierpsy Tracker on the test
data set:
Capture_Ch1_18062015_140908 Starting video compression.
ERROR:
ValueError: not enough values to unpack (expected 3, got 2)
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
Traceback (most recent call last):
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/ProcessWorker.py", line 108, in <module>
ProcessWorker(**args, cmd_original = subprocess.list2cmdline(sys.argv))
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/ProcessWorker.py", line 38, in __init__
self.execAllPoints()
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/ProcessWorker.py", line 66, in execAllPoints
cmd_original = self.cmd_original)
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/trackProvenance.py", line 28, in execThisPoint
func(**argkws)
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/analysis/compress/processVideo.py", line 142, in processVideo
compressVideo(video_file, masked_image_file, **compress_vid_param)
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/analysis/compress/compressVideo.py", line 366, in compressVideo
mask = getROIMask(img_reduce, **mask_param)
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/analysis/compress/compressVideo.py", line 76, in getROIMask
mask.copy(), cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
ValueError: not enough values to unpack (expected 3, got 2)
'/Users/tom/opt/anaconda3/envs/tierpsy/bin/python' '/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/ProcessWorker.py' '/Users/tom/Desktop/example_data/multiworm/Capture_Ch1_18062015_140908.mov' --masks_dir '/Users/tom/Tmp/MaskedVideos/' --results_dir '/Users/tom/Tmp/Results/' --json_file '/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/extras/param_files/MULTIWORM_OPENWORM.json' --analysis_checkpoints 'COMPRESS' 'TRAJ_CREATE' 'TRAJ_JOIN' 'SKE_INIT' 'BLOB_FEATS' 'SKE_CREATE' 'SKE_FILT' 'SKE_ORIENT' 'INT_PROFILE' 'INT_SKE_ORIENT' 'FEAT_CREATE'
*************************************************
Tasks: 1 finished, 0 remaining. Total_time 0:00:48.
*************************************************
So I copied and pasted that last subprocess command to the command line,
and got the following:
(tierpsy) Toms-MacBook-Pro:~ tom$ '/Users/tom/opt/anaconda3/envs/tierpsy/bin/python' '/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/ProcessWorker.py' '/Users/tom/Desktop/example_data/multiworm/Capture_Ch1_18062015_140908.mov' --masks_dir '/Users/tom/Tmp/MaskedVideos/' --results_dir '/Users/tom/Tmp/Results/' --json_file '/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/extras/param_files/MULTIWORM_OPENWORM.json' --analysis_checkpoints 'COMPRESS' 'TRAJ_CREATE' 'TRAJ_JOIN' 'SKE_INIT' 'BLOB_FEATS' 'SKE_CREATE' 'SKE_FILT' 'SKE_ORIENT' 'INT_PROFILE' 'INT_SKE_ORIENT' 'FEAT_CREATE'
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
Capture_Ch1_18062015_140908 Starting checkpoint: COMPRESS
COMPRESS
(1.0, 1.0, 'frames') (1.0, 'pixels') 1
Capture_Ch1_18062015_140908 Extracting video metadata...
Capture_Ch1_18062015_140908 Extracting video metadata. Total time = 0:00:14, fps = 37.0; Frame 500
Capture_Ch1_18062015_140908 Extracting video metadata. Total time = 0:00:29, fps = 32.4; Frame 1000
cannot read
Capture_Ch1_18062015_140908 Starting video compression.
Traceback (most recent call last):
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/ProcessWorker.py", line 108, in <module>
ProcessWorker(**args, cmd_original = subprocess.list2cmdline(sys.argv))
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/ProcessWorker.py", line 38, in __init__
self.execAllPoints()
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/ProcessWorker.py", line 66, in execAllPoints
cmd_original = self.cmd_original)
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/trackProvenance.py", line 28, in execThisPoint
func(**argkws)
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/analysis/compress/processVideo.py", line 142, in processVideo
compressVideo(video_file, masked_image_file, **compress_vid_param)
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/analysis/compress/compressVideo.py", line 366, in compressVideo
mask = getROIMask(img_reduce, **mask_param)
File "/Users/tom/opt/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/analysis/compress/compressVideo.py", line 76, in getROIMask
mask.copy(), cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
ValueError: not enough values to unpack (expected 3, got 2)
I saw in a closed post that some users had been having problems with
openCV. I'm using the latest version, openCV version 4.2.0 on macOS
Catalina 10.15.2. Could it be that Tierpsy is not compatible with the
newest openCV? If so, can you please advise as to how this can be fixed?
Thank you!
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I got the exactly same error as "ValueError: not enough values to unpack (expected 3, got 2)" while compressing the video after installation followed the given instruction. Did you update it in the condo-forge version now? If not, could you recommend me how to fix this error? Thank you! |
luigiferiani
added a commit
to luigiferiani/tierpsy-tracker
that referenced
this issue
Dec 3, 2021
* NN food detection: trying to improve on selection of the correct contour if the NN returns more than one area * making sure mask_file open for the minimum required amount of time in get_food_prob * changed get_food_contour_nn signature to avoid loading a model over and over again with possible memory leaks * Dockerfile: adding command to download trained food model from zenodo * Dockerfile: successfully added instructions to open tierpsy_gui after launching the container * getFoodContourNN.py: new algorithm is now implemented in the default Tierpsy pipeline
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I'm getting the following error when I use Tierpsy Tracker on the test data set:
So I copied and pasted that last subprocess command to the command line, and got the following:
I saw in a closed post that some users had been having problems with openCV. I'm using the latest version, openCV version 4.2.0 on macOS Catalina 10.15.2. Could it be that Tierpsy is not compatible with the newest openCV? If so, can you please advise as to how this can be fixed? Thank you!
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