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Still having drawing bug where masks wont actually be created once drawn

Open mayishazn opened this issue 1 year ago • 8 comments

I created a new environment and did a fresh install. The red circle does disappear once I close the loop but it doesn't turn into a mask. I've drawn four here and they're just stuck with the purple dotted lines. There is no drawing related output in the terminal either.

image

Originally posted by @mayishazn in https://github.com/MouseLand/cellpose/issues/961#issuecomment-2456358482

Also sorry for the repeat issue. It would just be highly convenient if I could fix masks on cellpose 3 directly.

mayishazn avatar Nov 14 '24 03:11 mayishazn

oh no, I was hoping I had found the bug! Does this happen when you start from scratch: can you delete your _seg.npy file and start labeling again and confirm it happens? can you also please export your environment conda env export > cp.yml and share it here? I will try to reproduce. how big is your image?

carsen-stringer avatar Nov 14 '24 18:11 carsen-stringer

name: freshcellpose3 channels:

  • pytorch
  • nvidia
  • defaults dependencies:
  • blas=1.0=mkl
  • bzip2=1.0.8=h2bbff1b_6
  • ca-certificates=2024.9.24=haa95532_0
  • console_shortcut=0.1.1=haa95532_6
  • cuda=11.6.1=0
  • cuda-cccl=11.6.55=0
  • cuda-command-line-tools=11.6.2=0
  • cuda-compiler=11.6.2=0
  • cuda-cudart=11.6.55=0
  • cuda-cudart-dev=11.6.55=0
  • cuda-cuobjdump=11.6.124=0
  • cuda-cupti=11.6.124=0
  • cuda-cuxxfilt=11.6.124=0
  • cuda-libraries=11.6.1=0
  • cuda-libraries-dev=11.6.1=0
  • cuda-memcheck=11.8.86=0
  • cuda-nsight-compute=12.4.1=0
  • cuda-nvcc=11.6.124=0
  • cuda-nvdisasm=12.6.77=0
  • cuda-nvml-dev=11.6.55=0
  • cuda-nvprof=12.6.80=0
  • cuda-nvprune=11.6.124=0
  • cuda-nvrtc=11.6.124=0
  • cuda-nvrtc-dev=11.6.124=0
  • cuda-nvtx=11.6.124=0
  • cuda-nvvp=12.6.80=0
  • cuda-runtime=11.6.1=0
  • cuda-sanitizer-api=12.6.77=0
  • cuda-toolkit=11.6.1=0
  • cuda-tools=11.6.1=0
  • cuda-version=12.6=3
  • cuda-visual-tools=11.6.1=0
  • expat=2.6.3=h5da7b33_0
  • fontconfig=2.14.1=hb33846d_3
  • freetype=2.12.1=ha860e81_0
  • gmpy2=2.1.2=py311h7f96b67_0
  • intel-openmp=2023.1.0=h59b6b97_46320
  • jinja2=3.1.4=py311haa95532_0
  • libcublas=11.9.2.110=0
  • libcublas-dev=11.9.2.110=0
  • libcufft=10.7.1.112=0
  • libcufft-dev=10.7.1.112=0
  • libcurand=10.3.7.77=0
  • libcurand-dev=10.3.7.77=0
  • libcusolver=11.3.4.124=0
  • libcusolver-dev=11.3.4.124=0
  • libcusparse=11.7.2.124=0
  • libcusparse-dev=11.7.2.124=0
  • libffi=3.4.4=hd77b12b_1
  • libglib=2.78.4=ha17d25a_0
  • libiconv=1.16=h2bbff1b_3
  • libnpp=11.6.3.124=0
  • libnpp-dev=11.6.3.124=0
  • libnvjpeg=11.6.2.124=0
  • libnvjpeg-dev=11.6.2.124=0
  • libpng=1.6.39=h8cc25b3_0
  • libuv=1.48.0=h827c3e9_0
  • libxml2=2.13.1=h24da03e_2
  • mkl=2023.1.0=h6b88ed4_46358
  • mpc=1.1.0=h7edee0f_1
  • mpfr=4.0.2=h62dcd97_1
  • mpir=3.0.0=hec2e145_1
  • mpmath=1.3.0=py311haa95532_0
  • nsight-compute=2024.3.2.3=0
  • openssl=3.0.15=h827c3e9_0
  • pcre2=10.42=h0ff8eda_1
  • pip=24.2=py311haa95532_0
  • python=3.11.10=h4607a30_0
  • pytorch-cuda=11.6=h867d48c_1
  • pytorch-mutex=1.0=cpu
  • pyyaml=6.0.2=py311h827c3e9_0
  • setuptools=75.1.0=py311haa95532_0
  • sqlite=3.45.3=h2bbff1b_0
  • tbb=2021.8.0=h59b6b97_0
  • tk=8.6.14=h0416ee5_0
  • typing_extensions=4.11.0=py311haa95532_0
  • tzdata=2024b=h04d1e81_0
  • vc=14.40=h2eaa2aa_1
  • vs2015_runtime=14.40.33807=h98bb1dd_1
  • wheel=0.44.0=py311haa95532_0
  • xz=5.4.6=h8cc25b3_1
  • yaml=0.2.5=he774522_0
  • zlib=1.2.13=h8cc25b3_1
  • pip:
    • cellpose==3.1.1.dev1+g9398cac
    • colorama==0.4.6
    • fastremap==1.15.0
    • filelock==3.16.1
    • fsspec==2024.10.0
    • imagecodecs==2024.9.22
    • llvmlite==0.43.0
    • markupsafe==3.0.2
    • natsort==8.4.0
    • networkx==3.4.2
    • numba==0.60.0
    • numpy==2.0.2
    • opencv-python-headless==4.10.0.84
    • packaging==24.1
    • pillow==10.2.0
    • pygments==2.18.0
    • pyqt6==6.7.1
    • pyqt6-qt6==6.7.3
    • pyqt6-sip==13.8.0
    • pyqtgraph==0.13.7
    • qtpy==2.4.2
    • roifile==2024.9.15
    • scipy==1.14.1
    • superqt==0.6.7
    • sympy==1.13.1
    • tifffile==2024.9.20
    • torch==2.5.1+cu118
    • torchaudio==2.5.1+cu118
    • torchvision==0.20.1+cu118
    • tqdm==4.66.6
    • typing-extensions==4.12.2 prefix: C:\Users\mayis\anaconda3\envs\freshcellpose3

mayishazn avatar Nov 15 '24 05:11 mayishazn

These are 2048x2048 images and some of them are zstacks with 10 slices. It seems to happen regardless of if I'm starting from scratch or fixing masks that cyto3 found. image

mayishazn avatar Nov 15 '24 05:11 mayishazn

idk if the image type matters? These are tiffs

mayishazn avatar Nov 15 '24 05:11 mayishazn

For the stacks are you opening them with --Zstack? In that case single stroke is off

carsen-stringer avatar Nov 15 '24 12:11 carsen-stringer

Yes I am opening them with --Zstack. So how do I edit them then?

mayishazn avatar Nov 18 '24 23:11 mayishazn

Ahha that's it, you have to press enter to complete the mask, or you can turn on single stroke

carsen-stringer avatar Nov 20 '24 01:11 carsen-stringer

image This works for a few masks and then it gets stuck on draw mode again.

mayishazn avatar Dec 04 '24 18:12 mayishazn