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added better memory caching, multithreaded processing, cleanup scripts dir

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rpotter6298
2026-03-13 08:08:36 +01:00
parent 8282461a23
commit 7ea85d5426
39 changed files with 1850 additions and 1998 deletions
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environment.yml
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name: fundus_imaging
channels:
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- alsa-lib=1.2.11=hd590300_1
- asttokens=2.4.1=pyhd8ed1ab_0
- attr=2.5.1=h166bdaf_1
- blas=1.0=openblas
- bottleneck=1.3.7=py312ha883a20_0
- brotli=1.0.9=h5eee18b_8
- brotli-bin=1.0.9=h5eee18b_8
- bzip2=1.0.8=hd590300_5
- ca-certificates=2025.9.9=h06a4308_0
- cairo=1.18.0=h3faef2a_0
- comm=0.2.2=pyhd8ed1ab_0
- contourpy=1.2.0=py312hdb19cb5_0
- cycler=0.11.0=pyhd3eb1b0_0
- dbus=1.13.18=hb2f20db_0
- debugpy=1.8.1=py312h30efb56_0
- decorator=5.1.1=pyhd8ed1ab_0
- exceptiongroup=1.2.0=pyhd8ed1ab_2
- executing=2.0.1=pyhd8ed1ab_0
- expat=2.6.2=h6a678d5_0
- font-ttf-dejavu-sans-mono=2.37=hd3eb1b0_0
- font-ttf-inconsolata=2.001=hcb22688_0
- font-ttf-source-code-pro=2.030=hd3eb1b0_0
- font-ttf-ubuntu=0.83=h8b1ccd4_0
- fontconfig=2.14.2=h14ed4e7_0
- fonts-anaconda=1=h8fa9717_0
- fonts-conda-ecosystem=1=hd3eb1b0_0
- fonttools=4.51.0=py312h5eee18b_0
- freetype=2.12.1=h4a9f257_0
- gettext=0.22.5=h59595ed_2
- gettext-tools=0.22.5=h59595ed_2
- glib=2.80.2=hf974151_0
- glib-tools=2.80.2=hb6ce0ca_0
- graphite2=1.3.14=h295c915_1
- gst-plugins-base=1.14.1=h6a678d5_1
- gstreamer=1.14.1=h5eee18b_1
- harfbuzz=8.5.0=hfac3d4d_0
- icu=73.2=h59595ed_0
- imageio=2.37.0=py312h06a4308_0
- importlib-metadata=7.1.0=pyha770c72_0
- importlib_metadata=7.1.0=hd8ed1ab_0
- ipykernel=6.29.3=pyhd33586a_0
- ipython=8.24.0=pyh707e725_0
- ipywidgets=8.1.2=pyhd8ed1ab_1
- jedi=0.19.1=pyhd8ed1ab_0
- joblib=1.4.0=py312h06a4308_0
- jpeg=9e=h5eee18b_1
- jupyter_client=8.6.1=pyhd8ed1ab_0
- jupyter_core=5.7.2=py312h7900ff3_0
- jupyterlab_widgets=3.0.10=py312h06a4308_0
- keyutils=1.6.1=h166bdaf_0
- kiwisolver=1.4.4=py312h6a678d5_0
- krb5=1.20.1=h81ceb04_0
- lame=3.100=h7b6447c_0
- lazy_loader=0.4=py312h06a4308_0
- lcms2=2.12=h3be6417_0
- ld_impl_linux-64=2.40=h55db66e_0
- lerc=3.0=h295c915_0
- libasprintf=0.22.5=h661eb56_2
- libasprintf-devel=0.22.5=h661eb56_2
- libbrotlicommon=1.0.9=h5eee18b_8
- libbrotlidec=1.0.9=h5eee18b_8
- libbrotlienc=1.0.9=h5eee18b_8
- libcap=2.69=h0f662aa_0
- libclang=14.0.6=default_hc6dbbc7_1
- libclang-cpp15=15.0.7=default_h127d8a8_5
- libclang13=14.0.6=default_he11475f_1
- libcups=2.4.2=h2d74bed_1
- libdeflate=1.17=h5eee18b_1
- libedit=3.1.20191231=he28a2e2_2
- libevent=2.1.12=hdbd6064_1
- libexpat=2.6.2=h59595ed_0
- libffi=3.4.2=h7f98852_5
- libflac=1.4.3=h59595ed_0
- libgcc-ng=13.2.0=h77fa898_7
- libgcrypt=1.10.3=hd590300_0
- libgettextpo=0.22.5=h59595ed_2
- libgettextpo-devel=0.22.5=h59595ed_2
- libgfortran=3.0.0=1
- libgfortran-ng=11.2.0=h00389a5_1
- libgfortran5=11.2.0=h1234567_1
- libglib=2.80.2=hf974151_0
- libgomp=13.2.0=h77fa898_7
- libgpg-error=1.49=h4f305b6_0
- libiconv=1.17=hd590300_2
- libjpeg-turbo=2.1.4=h166bdaf_0
- libllvm14=14.0.6=hdb19cb5_3
- libllvm15=15.0.7=hb3ce162_4
- libllvm18=18.1.5=hb77312f_0
- libnsl=2.0.1=hd590300_0
- libogg=1.3.5=h27cfd23_1
- libopenblas=0.3.21=h043d6bf_0
- libopus=1.3.1=h7b6447c_0
- libpng=1.6.43=h2797004_0
- libpq=12.17=hdbd6064_0
- libsndfile=1.2.2=hc60ed4a_1
- libsodium=1.0.18=h36c2ea0_1
- libsqlite=3.45.3=h2797004_0
- libstdcxx-ng=13.2.0=hc0a3c3a_7
- libsystemd0=255=h3516f8a_1
- libtiff=4.5.1=h6a678d5_0
- libuuid=2.38.1=h0b41bf4_0
- libvorbis=1.3.7=h7b6447c_0
- libwebp-base=1.3.2=h5eee18b_0
- libxcb=1.15=h7f8727e_0
- libxcrypt=4.4.36=hd590300_1
- libxkbcommon=1.7.0=h662e7e4_0
- libxml2=2.12.7=hc051c1a_0
- libzlib=1.2.13=hd590300_5
- lz4-c=1.9.4=h6a678d5_1
- matplotlib=3.8.4=py312h06a4308_0
- matplotlib-base=3.8.4=py312h526ad5a_0
- matplotlib-inline=0.1.7=pyhd8ed1ab_0
- mpg123=1.32.6=h59595ed_0
- mysql=5.7.20=hf484d3e_1001
- mysql-common=8.3.0=hf1915f5_4
- mysql-libs=8.3.0=hca2cd23_4
- ncurses=6.5=h59595ed_0
- nest-asyncio=1.6.0=pyhd8ed1ab_0
- networkx=3.4.2=py312h06a4308_0
- nspr=4.35=h6a678d5_0
- nss=3.100=hca3bf56_0
- numexpr=2.8.7=py312he7dcb8a_0
- numpy=1.26.4=py312h2809609_0
- numpy-base=1.26.4=py312he1a6c75_0
- openblas=0.3.4=ha44fe06_0
- openjpeg=2.4.0=h3ad879b_0
- openssl=3.3.0=hd590300_0
- packaging=24.0=pyhd8ed1ab_0
- pandas=2.2.1=py312h526ad5a_0
- parso=0.8.4=pyhd8ed1ab_0
- pcre2=10.43=hcad00b1_0
- pexpect=4.9.0=pyhd8ed1ab_0
- pickleshare=0.7.5=py_1003
- pillow=10.3.0=py312h5eee18b_0
- pixman=0.43.2=h59595ed_0
- platformdirs=4.2.1=pyhd8ed1ab_0
- ply=3.11=py312h06a4308_1
- prompt-toolkit=3.0.42=pyha770c72_0
- psutil=5.9.8=py312h98912ed_0
- ptyprocess=0.7.0=pyhd3deb0d_0
- pulseaudio-client=17.0=hb77b528_0
- pure_eval=0.2.2=pyhd8ed1ab_0
- pybind11-abi=5=hd3eb1b0_0
- pygments=2.18.0=pyhd8ed1ab_0
- pyparsing=3.0.9=py312h06a4308_0
- pyqt=5.15.10=py312h6a678d5_0
- pyqt5-sip=12.13.0=py312h5eee18b_0
- python=3.12.3=hab00c5b_0_cpython
- python-dateutil=2.9.0=pyhd8ed1ab_0
- python-tzdata=2023.3=pyhd3eb1b0_0
- python_abi=3.12=4_cp312
- pytz=2024.1=py312h06a4308_0
- pyzmq=26.0.3=py312h8fd38d8_0
- qt-main=5.15.2=h53bd1ea_10
- readline=8.2=h8228510_1
- scikit-image=0.25.2=py312hc74f9fe_0
- scikit-learn=1.4.2=py312h526ad5a_1
- scipy=1.13.0=py312h2809609_0
- setuptools=69.5.1=pyhd8ed1ab_0
- sip=6.7.12=py312h6a678d5_0
- six=1.16.0=pyh6c4a22f_0
- sqlite=3.45.3=h5eee18b_0
- stack_data=0.6.2=pyhd8ed1ab_0
- threadpoolctl=2.2.0=pyh0d69192_0
- tifffile=2024.12.12=py312h06a4308_0
- tk=8.6.13=noxft_h4845f30_101
- tornado=6.4=py312h98912ed_0
- traitlets=5.14.3=pyhd8ed1ab_0
- typing_extensions=4.11.0=pyha770c72_0
- tzdata=2024a=h0c530f3_0
- unicodedata2=15.1.0=py312h5eee18b_0
- wcwidth=0.2.13=pyhd8ed1ab_0
- widgetsnbextension=4.0.10=py312h06a4308_0
- xcb-util=0.4.0=hd590300_1
- xcb-util-image=0.4.0=h8ee46fc_1
- xcb-util-keysyms=0.4.0=h8ee46fc_1
- xcb-util-renderutil=0.3.9=hd590300_1
- xcb-util-wm=0.4.1=h8ee46fc_1
- xkeyboard-config=2.41=hd590300_0
- xlrd=2.0.1=pyhd3eb1b0_1
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.1.1=hd590300_0
- xorg-libsm=1.2.4=h7391055_0
- xorg-libx11=1.8.9=h8ee46fc_0
- xorg-libxau=1.0.11=hd590300_0
- xorg-libxext=1.3.4=h0b41bf4_2
- xorg-libxrender=0.9.11=hd590300_0
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h0b41bf4_1003
- xorg-xf86vidmodeproto=2.3.1=h7f98852_1002
- xorg-xproto=7.0.31=h27cfd23_1007
- xz=5.4.6=h5eee18b_1
- zeromq=4.3.5=h6a678d5_0
- zipp=3.17.0=pyhd8ed1ab_0
- zlib=1.2.13=hd590300_5
- zstd=1.5.6=ha6fb4c9_0
- pip:
- et-xmlfile==2.0.0
- opencv-python==4.9.0.80
- openpyxl==3.1.5
- pip==25.2
- pytorch-triton-rocm==3.2.0+rocm6.4.1.git6da9e660
- sympy==1.13.1
- torch==2.6.0+rocm6.4.1.git1ded221d
- torchaudio==2.6.0+rocm6.4.1.gitd8831425
- torchvision==0.21.0+rocm6.4.1.git4040d51f
- tqdm==4.66.4
- wheel==0.45.1
prefix: /home/rpotter/miniconda3/envs/fundus_imaging