ge-xing / Diff-UNet

Diff-UNet: A Diffusion Embedded Network for Volumetric Segmentation. (using diffusion for 3D medical image segmentation)
Apache License 2.0
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Request for requirements.txt #31

Open ZhengChen6 opened 6 months ago

ZhengChen6 commented 6 months ago

Could you please share your requirements.txt file, thank you!

ZhengChen6 commented 6 months ago

作者您好!由于您没有提供环境安装文件,我自己装的一些包或许因为版本更新的问题,导致test.py甚至无法运行起来,能否麻烦您提供一下您的环境配置文件,谢谢! @ge-xing

ge-xing commented 6 months ago

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file:///tmp/build/80754af9/qstylizer_1617713584600/work/dist/qstylizer-0.1.10-py2.py3-none-any.whl QtAwesome @ file:///tmp/build/80754af9/qtawesome_1637160816833/work qtconsole @ file:///opt/conda/conda-bld/qtconsole_1662018252641/work QtPy @ file:///opt/conda/conda-bld/qtpy_1662014892439/work qudida==0.0.4 queuelib==1.5.0 regex @ file:///tmp/abs_41f5bce5-0a2e-45aa-b231-1fd2fbd57753gfpe6sjm/croots/recipe/regex_1658257178822/work requests @ file:///opt/conda/conda-bld/requests_1657734628632/work requests-file @ file:///Users/ktietz/demo/mc3/conda-bld/requests-file_1629455781986/work requests-oauthlib==1.3.1 rich==13.7.0 rope @ file:///opt/conda/conda-bld/rope_1643788605236/work rsa==4.9 Rtree @ file:///tmp/build/80754af9/rtree_1618420843093/work ruamel-yaml-conda @ file:///tmp/build/80754af9/ruamel_yaml_1616016711199/work s3transfer @ file:///opt/conda/conda-bld/s3transfer_1654524197066/work safetensors==0.4.0 scikit-image @ file:///tmp/build/80754af9/scikit-image_1648214171611/work scikit-learn @ file:///tmp/build/80754af9/scikit-learn_1642617106979/work scikit-learn-intelex==2021.20221004.171807 scipy==1.9.1 Scrapy @ file:///tmp/abs_e3bmwi01y8/croots/recipe/scrapy_1659598696235/work seaborn @ file:///tmp/build/80754af9/seaborn_1629307859561/work SecretStorage @ file:///tmp/build/80754af9/secretstorage_1614022780358/work Send2Trash @ file:///tmp/build/80754af9/send2trash_1632406701022/work sentencepiece==0.1.99 sentry-sdk==1.40.0 service-identity @ file:///Users/ktietz/demo/mc3/conda-bld/service_identity_1629460757137/work setproctitle==1.3.3 shellingham==1.5.4 SimpleITK==2.3.1 sip @ file:///tmp/abs_44cd77b_pu/croots/recipe/sip_1659012365470/work six @ file:///tmp/build/80754af9/six_1644875935023/work smart-open @ file:///opt/conda/conda-bld/smart_open_1651563547610/work smmap==5.0.1 sniffio @ file:///tmp/build/80754af9/sniffio_1614030464178/work snowballstemmer @ file:///tmp/build/80754af9/snowballstemmer_1637937080595/work sortedcollections @ file:///tmp/build/80754af9/sortedcollections_1611172717284/work sortedcontainers @ file:///tmp/build/80754af9/sortedcontainers_1623949099177/work soupsieve @ file:///tmp/build/80754af9/soupsieve_1636706018808/work Sphinx @ file:///opt/conda/conda-bld/sphinx_1657784123546/work sphinxcontrib-applehelp @ file:///home/ktietz/src/ci/sphinxcontrib-applehelp_1611920841464/work sphinxcontrib-devhelp @ file:///home/ktietz/src/ci/sphinxcontrib-devhelp_1611920923094/work sphinxcontrib-htmlhelp @ file:///tmp/build/80754af9/sphinxcontrib-htmlhelp_1623945626792/work sphinxcontrib-jsmath @ file:///home/ktietz/src/ci/sphinxcontrib-jsmath_1611920942228/work sphinxcontrib-qthelp @ file:///home/ktietz/src/ci/sphinxcontrib-qthelp_1611921055322/work sphinxcontrib-serializinghtml @ file:///tmp/build/80754af9/sphinxcontrib-serializinghtml_1624451540180/work spyder @ file:///opt/conda/conda-bld/spyder_1663056818299/work spyder-kernels @ file:///opt/conda/conda-bld/spyder-kernels_1662457880976/work SQLAlchemy @ file:///tmp/abs_18b3238f-9c23-4182-a392-63af30a93c1er8j_yw60/croots/recipe/sqlalchemy_1657867856580/work statsmodels @ file:///tmp/build/80754af9/statsmodels_1648015433305/work sympy @ file:///tmp/build/80754af9/sympy_1647853653589/work tables @ file:///tmp/build/80754af9/pytables_1607975397488/work tabulate @ file:///opt/conda/conda-bld/tabulate_1657784105888/work tb-nightly==2.16.0a20240129 TBB==0.2 tblib @ file:///Users/ktietz/demo/mc3/conda-bld/tblib_1629402031467/work tenacity @ file:///tmp/abs_9ca5cd06-f53b-4ea6-8eea-954e11157fddo5mhurpp/croots/recipe/tenacity_1657899103026/work tensorboard-data-server==0.7.2 tensorrt==8.6.1.post1 tensorrt-bindings==8.6.1 tensorrt-libs==8.6.1 termcolor==2.4.0 terminado @ file:///tmp/build/80754af9/terminado_1644322582718/work testpath @ file:///opt/conda/conda-bld/testpath_1655908557405/work text-unidecode @ file:///Users/ktietz/demo/mc3/conda-bld/text-unidecode_1629401354553/work textdistance @ file:///tmp/build/80754af9/textdistance_1612461398012/work tf_keras-nightly==2.16.0.dev2024012910 threadpoolctl==3.3.0 three-merge @ file:///tmp/build/80754af9/three-merge_1607553261110/work tifffile @ file:///tmp/build/80754af9/tifffile_1627275862826/work timm==0.9.12 tinycss @ file:///tmp/build/80754af9/tinycss_1617713798712/work tldextract @ file:///opt/conda/conda-bld/tldextract_1646638314385/work tokenizers==0.14.1 toml @ file:///tmp/build/80754af9/toml_1616166611790/work tomli @ file:///opt/conda/conda-bld/tomli_1657175507142/work tomlkit @ file:///tmp/abs_56_0lnnq5x/croots/recipe/tomlkit_1658946880479/work toolz @ file:///tmp/build/80754af9/toolz_1636545406491/work torch==2.1.0 torch-fidelity==0.3.0 torchaudio==2.1.0 torchio==0.19.3 torchmetrics==1.2.1 torchvision==0.16.0 tornado @ file:///tmp/build/80754af9/tornado_1606942317143/work tqdm @ file:///opt/conda/conda-bld/tqdm_1664392687731/work traceback2==1.4.0 traitlets @ file:///tmp/build/80754af9/traitlets_1636710298902/work transformers==4.35.0 triton==2.1.0 ttach==0.0.3 Twisted @ file:///tmp/abs_82802zpkox/croots/recipe/twisted_1659592759417/work typer==0.9.0 typing_extensions @ file:///tmp/abs_ben9emwtky/croots/recipe/typing_extensions_1659638822008/work tzdata==2023.4 ujson @ file:///opt/conda/conda-bld/ujson_1657544923770/work Unidecode @ file:///tmp/build/80754af9/unidecode_1614712377438/work unittest2==1.1.0 urllib3 @ file:///tmp/abs_5dhwnz6atv/croots/recipe/urllib3_1659110457909/work w3lib @ file:///Users/ktietz/demo/mc3/conda-bld/w3lib_1629359764703/work wandb==0.16.2 watchdog @ file:///tmp/build/80754af9/watchdog_1638367282716/work wcwidth==0.2.13 webdataset==0.2.86 webencodings==0.5.1 websocket-client @ file:///tmp/build/80754af9/websocket-client_1614803975924/work Werkzeug @ file:///opt/conda/conda-bld/werkzeug_1645628268370/work whatthepatch @ file:///opt/conda/conda-bld/whatthepatch_1661795988879/work widgetsnbextension @ file:///tmp/build/80754af9/widgetsnbextension_1644992802045/work wrapt @ file:///tmp/abs_c335821b-6e43-4504-9816-b1a52d3d3e1eel6uae8l/croots/recipe/wrapt_1657814400492/work wurlitzer @ file:///tmp/build/80754af9/wurlitzer_1638368168359/work xarray @ file:///opt/conda/conda-bld/xarray_1639166117697/work xlrd @ file:///tmp/build/80754af9/xlrd_1608072521494/work XlsxWriter @ file:///opt/conda/conda-bld/xlsxwriter_1649073856329/work yapf @ file:///tmp/build/80754af9/yapf_1615749224965/work yarl==1.9.4 zict==2.1.0 zipp @ file:///opt/conda/conda-bld/zipp_1652341764480/work zope.interface @ file:///tmp/build/80754af9/zope.interface_1625036153595/work

ZhengChen6 commented 6 months ago

非常感谢您的分享!不过在您展示的requirements.txt文件中存在较多“@ file"的情况,这表示的是您的本地包,无法迁移到别的电脑上使用,我猜测您使用的应该是" pip freeze > requirements.txt" 这个命令,要解决这个问题,您可以尝试使用"pip list --format=freeze > requirements.txt"这个命令,用这个命令导出的将是包名及其版本号,而非本地包,能否麻烦您再次导出,谢谢! 您可以参考这个解决方法:https://blog.csdn.net/qq_36078992/article/details/109435000 @ge-xing

ge-xing commented 6 months ago

absl-py==2.0.0 accelerate==0.28.0 acvl-utils==0.2 addict==2.4.0 aiohttp==3.9.1 aiosignal==1.3.1 alabaster==0.7.12 albumentations==1.3.1 anaconda-client==1.11.0 anaconda-navigator==2.3.1 anaconda-project==0.11.1 antlr4-python3-runtime==4.9.3 anyio==3.5.0 appdirs==1.4.4 argon2-cffi==21.3.0 argon2-cffi-bindings==21.2.0 arrow==1.2.2 astroid==2.11.7 astropy==5.1 async-timeout==4.0.3 atomicwrites==1.4.0 attrs==21.4.0 auto_gptq==0.7.1 Automat==20.2.0 autopep8==1.6.0 Babel==2.9.1 backcall==0.2.0 backports.functools-lru-cache==1.6.4 backports.tempfile==1.0 backports.weakref==1.0.post1 batchgenerators==0.25 bcrypt==3.2.0 beautifulsoup4==4.11.1 binaryornot==0.4.4 bitarray==2.5.1 bkcharts==0.2 black==22.6.0 bleach==4.1.0 bokeh==2.4.3 boto3==1.24.28 botocore==1.27.28 Bottleneck==1.3.5 braceexpand==0.1.7 brotlipy==0.7.0 cachetools==5.3.2 causal-conv1d==1.0.0 certifi==2022.9.14 cffi==1.15.1 chardet==4.0.0 charset-normalizer==2.0.4 click==8.0.4 clip==1.0 cloudpickle==2.0.0 clyent==1.2.2 colorama==0.4.5 colorcet==3.0.0 coloredlogs==15.0.1 conda==22.9.0 conda-build==3.22.0 conda-content-trust==0.1.3 conda-pack==0.6.0 conda-package-handling==1.9.0 conda-repo-cli==1.0.20 conda-token==0.4.0 conda-verify==3.4.2 connected-components-3d==3.12.3 constantly==15.1.0 contextlib2==21.6.0 cookiecutter==1.7.3 cryptography==37.0.1 cssselect==1.1.0 cycler==0.11.0 Cython==0.29.32 cytoolz==0.11.0 daal4py==2021.6.0 dask==2022.7.0 dataclasses==0.6 datasets==2.14.7 datashader==0.14.1 datashape==0.5.4 debugpy==1.5.1 decorator==5.1.1 defusedxml==0.7.1 Deprecated==1.2.14 diff-match-patch==20200713 dill==0.3.7 distributed==2022.7.0 docker-pycreds==0.4.0 docutils==0.18.1 dynamic-network-architectures==0.2 einops==0.7.0 entrypoints==0.4 et-xmlfile==1.1.0 ExifRead-nocycle==3.0.1 fastjsonschema==2.16.2 filelock==3.6.0 fire==0.5.0 flake8==4.0.1 Flask==1.1.2 flatbuffers==23.5.26 fonttools==4.25.0 frozenlist==1.4.0 fsspec==2023.10.0 ftfy==6.1.3 future==0.18.2 gdown==5.0.1 gekko==1.0.7 gensim==4.1.2 gitdb==4.0.11 GitPython==3.1.41 glob2==0.7 gmpy2==2.1.2 google-auth==2.23.4 google-auth-oauthlib==1.1.0 grad-cam==1.4.8 greenlet==1.1.1 grpcio==1.59.2 h5py==3.7.0 HeapDict==1.0.1 holoviews==1.15.0 huggingface-hub==0.17.3 humanfriendly==10.0 humanize==4.9.0 hvplot==0.8.0 hyperlink==21.0.0 idna==3.3 imagecodecs==2021.8.26 imageio==2.19.3 imagesize==1.4.1 img2dataset==1.45.0 importlib-metadata==4.11.3 incremental==21.3.0 inflection==0.5.1 iniconfig==1.1.1 intake==0.6.5 intervaltree==3.1.0 ipykernel==6.15.2 ipython==7.31.1 ipython-genutils==0.2.0 ipywidgets==7.6.5 isort==5.9.3 itemadapter==0.3.0 itemloaders==1.0.4 itsdangerous==2.0.1 jdcal==1.4.1 jedi==0.18.1 jeepney==0.7.1 jellyfish==0.9.0 Jinja2==2.11.3 jinja2-time==0.2.0 jmespath==0.10.0 joblib==1.1.0 json5==0.9.6 jsonschema==4.16.0 jupyter==1.0.0 jupyter_client==7.3.4 jupyter-console==6.4.3 jupyter_core==4.11.1 jupyter-server==1.18.1 jupyterlab==3.4.4 jupyterlab-pygments==0.1.2 jupyterlab-server==2.10.3 jupyterlab-widgets==1.0.0 keyring==23.4.0 kiwisolver==1.4.2 lazy-object-proxy==1.6.0 libarchive-c==2.9 lightning-utilities==0.10.0 linecache2==1.0.0 llvmlite==0.38.0 lmdb==1.4.1 locket==1.0.0 lpips==0.1.4 lxml==4.9.1 lz4==3.1.3 mamba-ssm==1.0.1 Markdown==3.3.4 markdown-it-py==3.0.0 MarkupSafe==2.0.1 matplotlib==3.5.2 matplotlib-inline==0.1.6 mccabe==0.7.0 mdurl==0.1.2 MedPy==0.4.0 mistune==0.8.4 mkl-fft==1.3.1 mkl-random==1.2.2 mkl-service==2.4.0 ml-collections==0.1.1 mock==4.0.3 monai==1.3.0 mpmath==1.2.1 msgpack==1.0.3 multidict==6.0.4 multipledispatch==0.6.0 multiprocess==0.70.15 munkres==1.1.4 mypy-extensions==0.4.3 navigator-updater==0.3.0 nbclassic==0.3.5 nbclient==0.5.13 nbconvert==6.4.4 nbformat==5.5.0 nest-asyncio==1.5.5 networkx==2.8.4 nibabel==5.1.0 ninja==1.11.1.1 nltk==3.7 nose==1.3.7 notebook==6.4.12 numba==0.55.1 numexpr==2.8.3 numpy==1.24.4 numpydoc==1.4.0 nvidia-cublas-cu12==12.1.3.1 nvidia-cuda-cupti-cu12==12.1.105 nvidia-cuda-nvrtc-cu12==12.1.105 nvidia-cuda-runtime-cu12==12.1.105 nvidia-cudnn-cu12==8.9.2.26 nvidia-cufft-cu12==11.0.2.54 nvidia-curand-cu12==10.3.2.106 nvidia-cusolver-cu12==11.4.5.107 nvidia-cusparse-cu12==12.1.0.106 nvidia-nccl-cu12==2.18.1 nvidia-nvjitlink-cu12==12.3.52 nvidia-nvtx-cu12==12.1.105 oauthlib==3.2.2 olefile==0.46 omegaconf==2.3.0 onnx==1.15.0 onnxruntime==1.17.0 open-clip-torch==2.7.0 opencv-python==4.8.1.78 opencv-python-headless==4.9.0.80 openpyxl==3.1.2 packaging==21.3 pandas==2.2.0 pandocfilters==1.5.0 panel==0.13.1 param==1.12.0 parsel==1.6.0 parso==0.8.3 partd==1.2.0 pathlib==1.0.1 pathspec==0.9.0 patsy==0.5.2 peft==0.9.0 pep8==1.7.1 pexpect==4.8.0 pickleshare==0.7.5 Pillow==9.2.0 pip==22.2.2 pkginfo==1.8.2 platformdirs==2.5.2 plotly==5.9.0 pluggy==1.0.0 ply==3.11 poyo==0.5.0 prometheus-client==0.14.1 prompt-toolkit==3.0.20 Protego==0.1.16 protobuf==4.25.2 psutil==5.9.0 ptyprocess==0.7.0 py==1.11.0 pyarrow==15.0.0 pyarrow-hotfix==0.6 pyasn1==0.4.8 pyasn1-modules==0.2.8 pycocotools==2.0.7 pycodestyle==2.8.0 pycosat==0.6.3 pycparser==2.21 pyct==0.4.8 pycurl==7.45.1 PyDispatcher==2.0.5 pydocstyle==6.1.1 pyerfa==2.0.0 pyflakes==2.4.0 Pygments==2.17.2 PyHamcrest==2.0.2 PyJWT==2.4.0 pylint==2.14.5 pyls-spyder==0.4.0 pyodbc==4.0.34 pyOpenSSL==22.0.0 pyparsing==3.0.9 PyQt5-sip==12.11.0 pyrsistent==0.18.0 PySocks==1.7.1 pytest==7.1.2 python-dateutil==2.8.2 python-lsp-black==1.2.1 python-lsp-jsonrpc==1.0.0 python-lsp-server==1.5.0 python-slugify==5.0.2 python-snappy==0.6.0 pytorch-lightning==2.1.2 pytz==2022.1 pyviz-comms==2.0.2 PyWavelets==1.3.0 pyxdg==0.27 PyYAML==6.0 pyzmq==23.2.0 QDarkStyle==3.0.2 qstylizer==0.1.10 QtAwesome==1.0.3 qtconsole==5.3.2 QtPy==2.2.0 qudida==0.0.4 queuelib==1.5.0 regex==2022.7.9 requests==2.28.1 requests-file==1.5.1 requests-oauthlib==1.3.1 rich==13.7.0 rope==0.22.0 rouge==1.0.1 rsa==4.9 Rtree==0.9.7 ruamel-yaml-conda==0.15.100 s3transfer==0.6.0 safetensors==0.4.0 scikit-image==0.19.2 scikit-learn==1.0.2 scikit-learn-intelex==2021.20221004.171807 scipy==1.9.1 Scrapy==2.6.2 seaborn==0.11.2 SecretStorage==3.3.1 Send2Trash==1.8.0 sentencepiece==0.1.99 sentry-sdk==1.40.0 service-identity==18.1.0 setproctitle==1.3.3 setuptools==63.4.1 shellingham==1.5.4 SimpleITK==2.3.1 sip==6.6.2 six==1.16.0 smart-open==5.2.1 smmap==5.0.1 sniffio==1.2.0 snowballstemmer==2.2.0 sortedcollections==2.1.0 sortedcontainers==2.4.0 soupsieve==2.3.1 Sphinx==5.0.2 sphinxcontrib-applehelp==1.0.2 sphinxcontrib-devhelp==1.0.2 sphinxcontrib-htmlhelp==2.0.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5 spyder==5.3.3 spyder-kernels==2.3.3 SQLAlchemy==1.4.39 statsmodels==0.13.2 sympy==1.10.1 tables==3.6.1 tabulate==0.8.10 tb-nightly==2.16.0a20240129 TBB==0.2 tblib==1.7.0 tenacity==8.0.1 tensorboard-data-server==0.7.2 tensorrt==8.6.1.post1 tensorrt-bindings==8.6.1 tensorrt-libs==8.6.1 termcolor==2.4.0 terminado==0.13.1 testpath==0.6.0 text-unidecode==1.3 textdistance==4.2.1 tf_keras-nightly==2.16.0.dev2024012910 threadpoolctl==3.3.0 three-merge==0.1.1 tifffile==2021.7.2 timm==0.9.12 tinycss==0.4 tldextract==3.2.0 tokenizers==0.14.1 toml==0.10.2 tomli==2.0.1 tomlkit==0.11.1 toolz==0.11.2 torch==2.1.0 torch-fidelity==0.3.0 torchaudio==2.1.0 torchio==0.19.3 torchmetrics==1.2.1 torchvision==0.16.0 tornado==6.1 tqdm==4.64.1 traceback2==1.4.0 traitlets==5.1.1 transformers==4.35.0 triton==2.1.0 ttach==0.0.3 Twisted==22.2.0 typer==0.9.0 typing_extensions==4.3.0 tzdata==2023.4 ujson==5.4.0 Unidecode==1.2.0 unittest2==1.1.0 urllib3==1.26.11 w3lib==1.21.0 wandb==0.16.2 watchdog==2.1.6 wcwidth==0.2.13 webdataset==0.2.86 webencodings==0.5.1 websocket-client==0.58.0 Werkzeug==2.0.3 whatthepatch==1.0.2 wheel==0.37.1 widgetsnbextension==3.5.2 wrapt==1.14.1 wurlitzer==3.0.2 xarray==0.20.1 xlrd==2.0.1 XlsxWriter==3.0.3 xxhash==3.4.1 yapf==0.31.0 yarl==1.9.4 zict==2.1.0 zipp==3.8.0 zope.interface==5.4.0

ZhengChen6 commented 6 months ago

非常感谢您的分享!不过我尝试您的分享中缺失了一些包,例如blobfile,能否麻烦您检查一下您的conda环境是否正确,或者您可以尝试使用pipreqs这个包导出requirements.txt, cmd: "pipreqs ./ --encoding=utf8"。可以参考这个链接https://blog.csdn.net/qq295109601/article/details/121154733

不好意思实在麻烦您了!万分感激!!! @ge-xing

ge-xing commented 6 months ago

我认为这种小问题你可以自己解决一下,没必要跟我环境一致,而且这个代码也不需要什么复杂的环境。