Hi,
I have trouble analyzing a video using deeplabcut GUI. I am using my laptop with windows 8.1 pro. So I don’t have a GPU. It appears to be related to cropping but no matter how I change the cropping parameters, it did not work. Here is the info from the terminal https://docs.google.com/document/d/1KYBIXCE8jXVijMgGhdfD1GHOnUJXzmVMjwcO21Sjn6A/edit
Thanks!
could you share an image of the GUI screen and your config.yaml file?
still does not work
Overwriting cropping parameters: (0, 640, 277, 624)
These are used for all videos, but won’t be save to the cfg file.
Using snapshot-1000 for model C:\Users\QIAOLING\Desktop\OFT_11-Qiaoling-2020-04-
08\dlc-models\iteration-0\OFT_11Apr8-trainset95shuffle1
Initializing ResNet
INFO:tensorflow:Restoring parameters from C:\Users\QIAOLING\Desktop\OFT_11-Qiaol
ing-2020-04-08\dlc-models\iteration-0\OFT_11Apr8-trainset95shuffle1\train\snapsh
ot-1000
INFO:tensorflow:Restoring parameters from C:\Users\QIAOLING\Desktop\OFT_11-Qiaol
ing-2020-04-08\dlc-models\iteration-0\OFT_11Apr8-trainset95shuffle1\train\snapsh
ot-1000
Starting to analyze % C:\Users\QIAOLING\Videos\OFT_11_3.avi
Loading C:\Users\QIAOLING\Videos\OFT_11_3.avi
Duration of video [s]: 30.04 , recorded with 25.0 fps!
Overall # of frames: 751 found with (before cropping) frame dimensions: 928 5
76
Starting to extract posture
Cropping based on the x1 = 0 x2 = 640 y1 = 277 y2 = 624. You can adjust the crop
ping coordinates in the config.yaml file.
Traceback (most recent call last):
File “C:\Users\QIAOLING\Anaconda3\envs\dlc-windowsCPU\lib\site-packages\deepla
bcut\gui\analyze_videos.py”, line 264, in analyze_videos
destfolder=self.destfolder, crop=crop, dynamic=dynamic)
File “C:\Users\QIAOLING\Anaconda3\envs\dlc-windowsCPU\lib\site-packages\deepla
bcut\pose_estimation_tensorflow\predict_videos.py”, line 220, in analyze_videos
DLCscorer=AnalyzeVideo(video,DLCscorer,DLCscorerlegacy,trainFraction,cfg,dlc
_cfg,sess,inputs, outputs,pdindex,save_as_csv, destfolder,TFGPUinference,dynamic
)
File “C:\Users\QIAOLING\Anaconda3\envs\dlc-windowsCPU\lib\site-packages\deepla
bcut\pose_estimation_tensorflow\predict_videos.py”, line 497, in AnalyzeVideo
PredictedData,nframes=GetPoseF_GTF(cfg,dlc_cfg, sess, inputs, outputs,cap,nf
rames,int(dlc_cfg[“batch_size”]))
File “C:\Users\QIAOLING\Anaconda3\envs\dlc-windowsCPU\lib\site-packages\deepla
bcut\pose_estimation_tensorflow\predict_videos.py”, line 358, in GetPoseF_GTF
ny,nx=checkcropping(cfg,cap)
File “C:\Users\QIAOLING\Anaconda3\envs\dlc-windowsCPU\lib\site-packages\deepla
bcut\pose_estimation_tensorflow\predict_videos.py”, line 241, in checkcropping
raise Exception(‘Please check the boundary of cropping!’)
Exception: Please check the boundary of cropping!
If you suspect this is an IPython 7.12.0 bug, please report it at:
https://github.com/ipython/ipython/issues
or send an email to the mailing list at ipython-dev@python.org
You can print a more detailed traceback right now with “%tb”, or use “%debug”
to interactively debug it.
Extra-detailed tracebacks for bug-reporting purposes can be enabled via:
%config Application.verbose_crash=True
okay I think I see the issue; if one does not delete the cropping values in the config.yaml they will be used by default, due to this: https://github.com/AlexEMG/DeepLabCut/commit/6398f623b2b69a5df3eaf3bc8d5f4a70960962e9#diff-e1f7fa88206d6fd6451443092b057800
this is a bug, and I will fix it asap! For now, please change in your config.yaml file:
# Cropping Parameters (for analysis and outlier frame detection)
cropping: false
#if cropping is true for analysis, then set the values here:
x1: 0
x2: 640
y1: 277
y2: 624
TO:
# Cropping Parameters (for analysis and outlier frame detection)
cropping: false
#if cropping is true for analysis, then set the values here:
x1:
x2:
y1:
y2:
I appreciate very much your help! I tried but still didn’t go through… maybe my config file messed up
errors with analyzing a video.pdf (47.5 KB)
can you try to run this in the terminal (in your DLC env):
ipython
import deeplabcut
deeplabcut.__version__
cfp = r'C:\Users\QIAOLING\Desktop\OFT_11-Qiaoling-2020-04-
08\config.yaml'
deeplabcut.analyze_videos(cfp, [r'C:\Users\QIAOLING\Videos\OFT_11_3.avi'])
and let me know the output?
Look like it is working!! Just takes time
(base) C:\windows\system32>cd C:\Users\QIAOLING\Desktop\DeepLabCut\conda-environ
ments
(base) C:\Users\QIAOLING\Desktop\DeepLabCut\conda-environments>activate dlc-wind
owsCPU
(dlc-windowsCPU) C:\Users\QIAOLING\Desktop\DeepLabCut\conda-environments>ipython
Python 3.6.10 |Anaconda, Inc.| (default, Jan 7 2020, 15:18:16) [MSC v.1916 64 b
it (AMD64)]
Type ‘copyright’, ‘credits’ or ‘license’ for more information
IPython 7.12.0 – An enhanced Interactive Python. Type ‘?’ for help.
In [1]: import deeplabcut
In [2]: deeplabcut.version
Out[2]: ‘2.1.6.2’
In [3]: cfp = r’C:\Users\QIAOLING\Desktop\OFT_11-Qiaoling-2020-04-^M
…: 08\config.yaml’
File “”, line 1
cfp = r’C:\Users\QIAOLING\Desktop\OFT_11-Qiaoling-2020-04-
^
SyntaxError: EOL while scanning string literal
In [4]: cfp = r’C:\Users\QIAOLING\Desktop\OFT_11-Qiaoling-2020-04-08\config.yam
…: l’
In [5]: deeplabcut.analyze_videos(cfp, [r’C:\Users\QIAOLING\Videos\OFT_11_3.avi
…: '])
Using snapshot-1000 for model C:\Users\QIAOLING\Desktop\OFT_11-Qiaoling-2020-04-
08\dlc-models\iteration-0\OFT_11Apr8-trainset95shuffle1
Initializing ResNet
INFO:tensorflow:Restoring parameters from C:\Users\QIAOLING\Desktop\OFT_11-Qiaol
ing-2020-04-08\dlc-models\iteration-0\OFT_11Apr8-trainset95shuffle1\train\snapsh
ot-1000
INFO:tensorflow:Restoring parameters from C:\Users\QIAOLING\Desktop\OFT_11-Qiaol
ing-2020-04-08\dlc-models\iteration-0\OFT_11Apr8-trainset95shuffle1\train\snapsh
ot-1000
Starting to analyze % C:\Users\QIAOLING\Videos\OFT_11_3.avi
Loading C:\Users\QIAOLING\Videos\OFT_11_3.avi
Duration of video [s]: 30.04 , recorded with 25.0 fps!
Overall # of frames: 751 found with (before cropping) frame dimensions: 928 5
76
Starting to extract posture
11%|████▎ | 80/751 [06:28<57:13, 5.12s/it]
great, I will make a fix in the GUI soon, good catch, thanks 
glad it’s working; since your model is trained, you can also make a simple script that you can run to analyze new videos anytime they are placed inside a folder or subfolder!
Just edit the variables that would matter to you (here is the file you can download: https://github.com/DeepLabCut/DLCutils/blob/master/SCALE_YOUR_ANALYSIS/scale_analysis_oversubfolders.py) and then you can just run in the terminal:
(DLC-CPU) your com name$: python3 scale_analysis_oversubfolders.py
and it would analyze all the videos in the folder (and any subfolders) of any file type, i.e. avi, mp4, etc).
Great, very nice of you spending time troubleshooting!!
Actually one more quick question, so logitech webcam is not a good camera for the DLC analysis, right? I saw this “OpenCV and moviepy both have issues using logitech webcams, see post: https://github.com/AlexEMG/DeepLabCut/pull/476#issuecomment-551788921. It may appear to work fine, but you may have issues creating labeled videos with these types of videos as it does not detect the FPS correctly!” I tried with those videos and it did not seem to work well for the evaluation step as I remember. Unfortunately the behavior videos we previously collected are all from logitech webcam.
I have not tried myself, but you likely could export to an mp4 with h264 compression first?
hm, can try! thanks again!