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DeepLabCut / napari-deeplabcut

a napari plugin for labeling and refining keypoint data within DeepLabCut projects
GNU Lesser General Public License v3.0
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Body parts not being displayed in Napari GUI when trying to label frames #141

Open thewangshu opened 2 months ago

thewangshu commented 2 months ago

Hi, these are the necessary specs. Kindly let me know if you would require anything else that would help you resolve this bug.

OS: Windows 10 GPU : Nvidia GeForce RTX 3090 Memory: 128 GB DLC Version: 2.3.9 Python Version: 3.9.0 Napari Version: 0.4.18 Matplotlib version: 3.5.2 Numpy version: 1.23.4

Initially even labelling frames was a problem as Napari was not loading but after successfully installing the napari-deeplabcut and selecting it as well, the body parts are not being displayed.

I'm aware that this similar issue has been faced by others as well and the fixes provided in terms of updating the napari version and reinstalling DLC have all been attempted by me already. I even tried dragging and pasting the config.yaml file into the napari canvas (by running anaconda prompt without admin privileges) but that did not yield anything either. I am still left with no body parts being showing in the napari gui. Please find below a screenshot of the anaconda prompt as well as the napari gui. Any help would be hugely appreciated. I also tried reinstalling DLC in the hope that it would fix the error and here is a list of the things it reinstalled:

Requirement already satisfied: deeplabcut==2.3.9 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut[gui]==2.3.9) (2.3.9)
Requirement already satisfied: dlclibrary>=0.0.6 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.0.6)
Requirement already satisfied: filterpy>=1.4.4 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.4.5)
Requirement already satisfied: ruamel.yaml>=0.15.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.18.6)
Requirement already satisfied: imgaug>=0.4.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.4.0)
Requirement already satisfied: imageio-ffmpeg in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.5.1)
Requirement already satisfied: numba>=0.54 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.60.0)
Requirement already satisfied: matplotlib!=3.7.0,!=3.7.1,>=3.3 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (3.5.2)
Requirement already satisfied: networkx>=2.6 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (3.2.1)
Requirement already satisfied: numpy>=1.18.5 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.23.4)
Requirement already satisfied: pandas!=1.5.0,>=1.0.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (2.2.2)
Requirement already satisfied: scikit-image>=0.17 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.24.0)
Requirement already satisfied: scikit-learn>=1.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.5.1)
Requirement already satisfied: scipy>=1.9 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.13.1)
Requirement already satisfied: statsmodels>=0.11 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.14.2)
Requirement already satisfied: tables>=3.7.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (3.9.2)
Requirement already satisfied: torch<=1.12 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.12.0)
Requirement already satisfied: tensorpack>=0.11 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.11)
Requirement already satisfied: tf-slim>=1.1.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.1.0)
Requirement already satisfied: tqdm in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (4.66.5)
Requirement already satisfied: pyyaml in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (6.0.2)
Requirement already satisfied: Pillow>=7.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (10.4.0)
Requirement already satisfied: pyside6<6.3.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut[gui]==2.3.9) (6.3.1)
Requirement already satisfied: qdarkstyle==3.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut[gui]==2.3.9) (3.1)
Requirement already satisfied: napari-deeplabcut>=0.2.1.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut[gui]==2.3.9) (0.2.1.7)
Requirement already satisfied: qtpy>=1.9 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from qdarkstyle==3.1->deeplabcut[gui]==2.3.9) (2.4.1)
Requirement already satisfied: huggingface-hub in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from dlclibrary>=0.0.6->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.24.5)
Requirement already satisfied: six in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from imgaug>=0.4.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.16.0)
Requirement already satisfied: opencv-python in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from imgaug>=0.4.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (4.10.0.84)
Requirement already satisfied: imageio in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from imgaug>=0.4.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (2.35.0)
Requirement already satisfied: Shapely in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from imgaug>=0.4.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (2.0.5)
Requirement already satisfied: cycler>=0.10 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from matplotlib!=3.7.0,!=3.7.1,>=3.3->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from matplotlib!=3.7.0,!=3.7.1,>=3.3->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (4.53.1)
Requirement already satisfied: kiwisolver>=1.0.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from matplotlib!=3.7.0,!=3.7.1,>=3.3->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.4.5)
Requirement already satisfied: packaging>=20.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from matplotlib!=3.7.0,!=3.7.1,>=3.3->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (24.1)
Requirement already satisfied: pyparsing>=2.2.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from matplotlib!=3.7.0,!=3.7.1,>=3.3->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (3.1.2)
Requirement already satisfied: python-dateutil>=2.7 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from matplotlib!=3.7.0,!=3.7.1,>=3.3->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (2.9.0.post0)
Requirement already satisfied: dask-image in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (2024.5.3)
Requirement already satisfied: napari==0.4.18 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.4.18)
Requirement already satisfied: natsort in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (8.4.0)
Requirement already satisfied: opencv-python-headless in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (4.10.0.84)
Requirement already satisfied: appdirs>=1.4.4 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (1.4.4)
Requirement already satisfied: app-model<0.3.0,>=0.1.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.2.8)
Requirement already satisfied: cachey>=0.2.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.2.1)
Requirement already satisfied: certifi>=2018.1.18 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (2024.7.4)
Requirement already satisfied: dask!=2.28.0,>=2.15.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from dask[array]!=2.28.0,>=2.15.0->napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (2024.8.0)
Requirement already satisfied: jsonschema>=3.2.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (4.23.0)
Requirement already satisfied: lazy-loader>=0.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.4)
Requirement already satisfied: magicgui>=0.3.6 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.9.1)
Requirement already satisfied: napari-console>=0.0.6 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.0.9)
Requirement already satisfied: napari-plugin-engine>=0.1.9 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.2.0)
Requirement already satisfied: napari-svg>=0.1.7 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.2.0)
Requirement already satisfied: npe2>=0.5.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.7.7)
Requirement already satisfied: numpydoc>=0.9.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (1.5.0)
Requirement already satisfied: pint>=0.17 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.24.3)
Requirement already satisfied: psutil>=5.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (6.0.0)
Requirement already satisfied: psygnal>=0.3.4 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.11.1)
Requirement already satisfied: pydantic<2,>=1.9.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (1.10.17)
Requirement already satisfied: pygments>=2.6.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (2.18.0)
Requirement already satisfied: PyOpenGL>=3.1.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (3.1.7)
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Requirement already satisfied: tifffile>=2020.2.16 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (2024.8.10)
Requirement already satisfied: toolz>=0.10.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.12.1)
Requirement already satisfied: typing-extensions>=4.2.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (4.12.2)
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Requirement already satisfied: shiboken6==6.3.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from pyside6<6.3.2->deeplabcut[gui]==2.3.9) (6.3.1)
Requirement already satisfied: PySide6-Essentials==6.3.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from pyside6<6.3.2->deeplabcut[gui]==2.3.9) (6.3.1)
Requirement already satisfied: PySide6-Addons==6.3.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from pyside6<6.3.2->deeplabcut[gui]==2.3.9) (6.3.1)
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image image

MMathisLab commented 2 months ago

it looks like in your screen shot you don't have the deeplabcut-plugin enabled; you would see more widgets.

Can you check this to be sure it's installed: https://deeplabcut.github.io/DeepLabCut/docs/gui/napari_GUI.html

then be sure to activate the plugin:

Then, activate the plugin in Plugins > napari-deeplabcut: Keypoint controls.

thewangshu commented 2 months ago

Hi guys, I made sure to have napari-deeplabcut: Keypoint controls. plugin enabled. Please find below the screenshots of the same as well as the error napari gui spits out when trying to load the folder with extracted frames.

image image

MMathisLab commented 2 months ago

I'm convinced it's an installation or activation issue. In each image you share I don't see the correct controls.

https://deeplabcut.github.io/DeepLabCut/docs/beginner-guides/labeling.html

Here is what it should look like; do you ever see all these options?

I see you're running an older version of deeplabcut; are you using Python 3.10?

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thewangshu commented 2 months ago

Hi, in order to continue using Tensorflow I installed python 3.9.0 and subsequently installed DLC_2.3.9 as it worked perfectly fine for us before.

I'm assuming that there is a Napari version mismatch because of which this is happening. Can you please help accordingly as we want to continue using tensorflow with windows 10 as it worked perfectly fine for us.

n-poulsen commented 2 months ago

@thewangshu could you run napari --info in your conda environment and report the output? I think the issue is that pyside6==6.3.1 is installed, while currently we require pyside6==6.4.2 is required (see the homepage)