libtiff-5.dll error

[YasMakH]

Hi, I followed the instructions of this recent tutorial ( http://www.andrewjanowczyk.com/tutorial-quick-annotator-for-tubule-segmentation/ ) to install quick annotator in an anaconda environment, but when I run QA.py, I get an error about libtiff-5.dll not found. Any help ?

[tasvora]

Hi, Sorry to hear you are having an issue. What is your environment configuration like Windows/Linux ?? Cuda ? Can you send your console error log and your requirments.txt file

Regards Tasneem

[YasMakH]

I am using windows. following the tutorial instructions, I got cuda 11 ( using nvidia-smi), so I followed with cuda_11, and installed the corresponding requirements : cd cuda_11 pip3 install -r requirements.txt

the error in the console is as following :

_(annotator) C:\QuickAnnotator>python QA.py Config sections = ['common', 'flask', 'cuda', 'sqlalchemy', 'pooling', 'train_ae', 'train_tl', 'make_patches', 'make_embed', 'get_prediction', 'frontend', 'superpixel'] Traceback (most recent call last): File "QA.py", line 11, in from QA_api import api,delete_image File "C:\QuickAnnotator\QA_api.py", line 21, in from QA_utils import get_file_tail File "C:\QuickAnnotator\QAutils.py", line 1, in import torch File "C:\Users\Me\AppData\Local\Programs\Python\Python37\lib\site-packages\torch__init__.py", line 134, in raise err OSError: [WinError 126] The specified module could not be found. Error loading "C:\Users\3055366\AppData\Local\Programs\Python\Python37\lib\site-packages\torch\lib\libtiff-5.dll" or one of its dependencies.

[tasvora]

Can you please do a

pip freeze > env_requirements.txt This will generate a env_requirements.txt and please send us your env_requirements.txt file

[YasMakH]

Thank you. This is what I got my env_requirements.txt : absl-py==0.9.0 albumentations==0.4.3 altgraph==0.17 appJar==0.94.0 asciitree==0.3.3 astor==0.8.1 astroid==2.4.2 backcall==0.2.0 beautifulsoup4==4.8.2 blis==0.4.1 cachetools==4.0.0 catalogue==1.0.0 catalyst==20.12 certifi==2019.11.28 cffi==1.14.3 chardet==3.0.4 click==7.1.2 colorama==0.4.3 config==0.4.2 crank==0.8.1 cycler==0.10.0 cymem==2.0.3 decorator==4.4.2 fasteners==0.15 fastprogress==0.2.2 Flask==1.1.2 Flask-Restless==0.17.0 Flask-SQLAlchemy==2.4.4 future==0.18.2 gast==0.2.2 google-auth==1.11.2 google-auth-oauthlib==0.4.1 google-pasta==0.1.8 graphviz==0.8.4 grpcio==1.27.2 h5py==2.10.0 idna==2.6 imageio==2.8.0 imgaug==0.2.6 importlib-metadata==1.5.0 ipykernel==5.3.4 ipython==7.18.1 ipython-genutils==0.2.0 isort==5.6.4 itsdangerous==2.0.1 jedi==0.17.2 Jinja2==3.0.3 joblib==0.14.1 jupyter-client==6.1.7 jupyter-core==4.6.3 Kajiki==0.8.2 Keras==2.1.6 Keras-Applications==1.0.8 Keras-Preprocessing==1.1.0 kiwisolver==1.1.0 lazy-object-proxy==1.4.3 llvmlite==0.37.0 Markdown==3.2.1 MarkupSafe==2.0.1 matplotlib==3.1.3 mccabe==0.6.1 mimerender==0.6.0 monotonic==1.5 murmurhash==1.0.2 mxnet==1.5.0 networkx==2.4 nine==1.1.0 numba==0.54.1 numcodecs==0.7.2 numexpr==2.7.1 numpy==1.17.3 nvidia-ml-py3==7.352.0 oauthlib==3.1.0 opencv-contrib-python-headless==4.5.1.48 opencv-python==4.2.0.32 opencv-python-headless==4.5.4.60 opt-einsum==3.1.0 packaging==20.1 pandas==1.2.0 parso==0.7.1 pefile==2019.4.18 pickleshare==0.7.5 Pillow==8.1.2 plac==1.1.3 preshed==3.0.2 prompt-toolkit==3.0.7 protobuf==3.11.3 pyasn1==0.4.8 pyasn1-modules==0.2.8 pycparser==2.20 Pygments==2.7.1 PyInstaller==3.6 pylint==2.6.0 pyparsing==2.4.6 python-dateutil==2.8.1 python-mimeparse==1.6.0 pytz==2019.3 PyWavelets==1.1.1 pywin32-ctypes==0.2.0 PyYAML==5.3 pyzmq==19.0.2 repoze.lru==0.7 requests==2.25.1 requests-oauthlib==1.3.0 rsa==4.0 scikit-image==0.18.1 scikit-learn==0.24.0 scipy==1.6.0 six==1.14.0 soupsieve==2.0 spacy==2.2.3 SQLAlchemy==1.3.22 srsly==1.0.1 tensorboard==2.4.1 tensorboard-plugin-wit==1.8.0 tensorboardX==2.1 tensorflow==2.1.0 tensorflow-estimator==2.1.0 termcolor==1.1.0 thinc==7.3.1 threadpoolctl==3.0.0 tifffile==2021.11.2 toml==0.10.2 torch==1.8.1+cu111 torchaudio==0.8.1 torchvision==0.9.1+cu111 tornado==6.0.4 tqdm==4.43.0 traitlets==5.0.4 ttach==0.0.2 TurboGears2==2.4.3 typed-ast==1.4.1 typing-extensions==4.0.1 umap-learn==0.3.10 urllib3==1.22 wasabi==0.6.0 wcwidth==0.2.5 WebOb==1.8.6 Werkzeug==1.0.0 wrapt==1.12.0 zarr==2.5.0 zipp==3.0.0

[tasvora]

Hi

Thanks for this , and it looks alright, but seems like there is an issue in your environment. As I tried a brand new virtual environment and it works fine, and in your case the application is not even starting up.

Is there a possibility to create a new virtual environment and try this out? Are you already using a virtual environment ? we also do have a Docker file if you want to try it out with Docker.

[tasvora]

Hi Did it work ?

[YasMakH]

Unfortunately no. I repeated the process multiple times, on new environments, but still getting the same error related to libtiff-5.dll

[tasvora]

Is the error message the exact same ? and it occurs on run python QA.py?

[YasMakH]

Is the error message the exact same ? and it occurs on run python QA.py?

Yes. It is exactly the same, and occurs when running QA.py.

[tasvora]

Just noticed you are using python 3.7 ? is it possible to upgrade to python 3.8.

Also can you try the cpu version of pytorch and test it out

conda install pytorch torchvision torchaudio cpuonly -c pytorch or pip3 install torch torchvision torchaudio

[YasMakH]

C:\Users\3055366\AppData\Local\Programs\Python\Python37\lib\site-packages\torch\lib\libtiff-5.dll

Yes. I upgraded to python 3.8 following the same steps, and it is working now. Many thanks

[choosehappy]

Great, thanks for update!