diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..6174c26 --- /dev/null +++ b/environment.yml @@ -0,0 +1,25 @@ +name: pulmonary-tree-labeling +channels: + - pytorch + - nvidia + - conda-forge + - defaults +dependencies: + - python=3.9 + - pip + - pytorch=1.13.0 + - torchvision=0.14.0 + - torchaudio=0.13.0 + - pytorch-cuda=11.7 + - numpy + - pillow + - requests + - tqdm + - networkx + - psutil + - pip: + - torch-geometric==2.6.1 + - monai==1.4.0 + - nibabel==5.3.2 + - openpyxl==3.1.5 + - cupy-cuda12x==13.3.0 diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..d4f557b --- /dev/null +++ b/requirements.txt @@ -0,0 +1,26 @@ +# Python dependencies for pulmonary-tree-labeling +# Install with: pip install -r requirements.txt + +# Deep Learning +torch>=1.13.0 +torchvision>=0.14.0 +torchaudio>=0.13.0 +torch-geometric==2.6.1 + +# Medical Imaging +monai==1.4.0 +nibabel==5.3.2 + +# Data Processing +numpy>=1.26.0 +pillow>=10.0.0 +openpyxl==3.1.5 + +# Utilities +tqdm>=4.66.0 +networkx>=3.0 +psutil>=6.0.0 +requests>=2.32.0 + +# Optional: GPU acceleration (requires CUDA) +# cupy-cuda12x==13.3.0 diff --git a/requirments.txt b/requirments.txt deleted file mode 100644 index 69d3a9f..0000000 --- a/requirments.txt +++ /dev/null @@ -1,108 +0,0 @@ -# This file may be used to create an environment using: -# $ conda create --name --file -# platform: linux-64 -_libgcc_mutex=0.1=main -_openmp_mutex=5.1=1_gnu -aiohappyeyeballs=2.4.3=pypi_0 -aiohttp=3.10.10=pypi_0 -aiosignal=1.3.1=pypi_0 -async-timeout=4.0.3=pypi_0 -attrs=24.2.0=pypi_0 -blas=1.0=mkl -brotli-python=1.0.9=py39h6a678d5_8 -bzip2=1.0.8=h5eee18b_6 -ca-certificates=2024.9.24=h06a4308_0 -certifi=2024.8.30=py39h06a4308_0 -charset-normalizer=3.3.2=pyhd3eb1b0_0 -cuda-cudart=11.7.99=0 -cuda-cupti=11.7.101=0 -cuda-libraries=11.7.1=0 -cuda-nvrtc=11.7.99=0 -cuda-nvtx=11.7.91=0 -cuda-runtime=11.7.1=0 -cuda-version=12.6=3 -cupy-cuda12x=13.3.0=pypi_0 -et-xmlfile=2.0.0=pypi_0 -fastrlock=0.8.2=pypi_0 -ffmpeg=4.3=hf484d3e_0 -freetype=2.12.1=h4a9f257_0 -frozenlist=1.5.0=pypi_0 -fsspec=2024.10.0=pypi_0 -gmp=6.2.1=h295c915_3 -gnutls=3.6.15=he1e5248_0 -idna=3.7=py39h06a4308_0 -importlib-resources=6.4.5=pypi_0 -intel-openmp=2023.1.0=hdb19cb5_46306 -jinja2=3.1.4=pypi_0 -jpeg=9e=h5eee18b_3 -lame=3.100=h7b6447c_0 -lcms2=2.12=h3be6417_0 -ld_impl_linux-64=2.40=h12ee557_0 -lerc=3.0=h295c915_0 -libcublas=11.10.3.66=0 -libcufft=10.7.2.124=h4fbf590_0 -libcufile=1.11.1.6=0 -libcurand=10.3.7.77=0 -libcusolver=11.4.0.1=0 -libcusparse=11.7.4.91=0 -libdeflate=1.17=h5eee18b_1 -libffi=3.4.4=h6a678d5_1 -libgcc-ng=11.2.0=h1234567_1 -libgomp=11.2.0=h1234567_1 -libiconv=1.16=h5eee18b_3 -libidn2=2.3.4=h5eee18b_0 -libnpp=11.7.4.75=0 -libnvjpeg=11.8.0.2=0 -libpng=1.6.39=h5eee18b_0 -libstdcxx-ng=11.2.0=h1234567_1 -libtasn1=4.19.0=h5eee18b_0 -libtiff=4.5.1=h6a678d5_0 -libunistring=0.9.10=h27cfd23_0 -libwebp-base=1.3.2=h5eee18b_1 -lz4-c=1.9.4=h6a678d5_1 -markupsafe=3.0.2=pypi_0 -mkl=2023.1.0=h213fc3f_46344 -mkl-service=2.4.0=py39h5eee18b_1 -mkl_fft=1.3.10=py39h5eee18b_0 -mkl_random=1.2.7=py39h1128e8f_0 -monai=1.4.0=pypi_0 -multidict=6.1.0=pypi_0 -ncurses=6.4=h6a678d5_0 -nettle=3.7.3=hbbd107a_1 -networkx=3.2.1=pypi_0 -nibabel=5.3.2=pypi_0 -numpy=1.26.4=pypi_0 -openh264=2.1.1=h4ff587b_0 -openjpeg=2.5.2=he7f1fd0_0 -openpyxl=3.1.5=pypi_0 -openssl=3.0.15=h5eee18b_0 -packaging=24.1=pypi_0 -pillow=10.4.0=py39h5eee18b_0 -pip=24.2=py39h06a4308_0 -propcache=0.2.0=pypi_0 -psutil=6.1.0=pypi_0 -pyparsing=3.2.0=pypi_0 -pysocks=1.7.1=py39h06a4308_0 -python=3.9.20=he870216_1 -pytorch=1.13.0=py3.9_cuda11.7_cudnn8.5.0_0 -pytorch-cuda=11.7=h778d358_5 -pytorch-mutex=1.0=cuda -readline=8.2=h5eee18b_0 -requests=2.32.3=py39h06a4308_0 -setuptools=75.1.0=py39h06a4308_0 -sqlite=3.45.3=h5eee18b_0 -tbb=2021.8.0=hdb19cb5_0 -tk=8.6.14=h39e8969_0 -torch-geometric=2.6.1=pypi_0 -torchaudio=0.13.0=py39_cu117 -torchvision=0.14.0=py39_cu117 -tqdm=4.66.5=pypi_0 -typing_extensions=4.11.0=py39h06a4308_0 -tzdata=2024b=h04d1e81_0 -urllib3=2.2.3=py39h06a4308_0 -wheel=0.44.0=py39h06a4308_0 -xz=5.4.6=h5eee18b_1 -yarl=1.16.0=pypi_0 -zipp=3.20.2=pypi_0 -zlib=1.2.13=h5eee18b_1 -zstd=1.5.6=hc292b87_0