ver228
commented
4 years ago 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 notifications@github.com 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
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
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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zhaoyuan98
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!