diff --git a/README.md b/README.md index 4034ec5..45eada8 100644 --- a/README.md +++ b/README.md @@ -43,6 +43,8 @@

UMBRAE decodes multimodal explanations from brain signals. (1) We introduce a universal brain encoder for multimodal-brain alignment and recover conceptual and spatial details by using multimodal large language models. (2) We introduce cross-subject training to overcome unique brain patterns of different individuals. This allows brain signals from multiple subjects to be trained within the same model This allows brain signals from multiple subjects to be trained within the same model. (3) Our method supports weakly-supervised subject adaptation, enabling the training of a model for a new subject in a data-efficient manner. (4) For evaluation, we introduce BrainHub, a brain understanding benchmark, based on NSD and COCO. ## News :triangular_flag_on_post: +- [2024/04/16] Provide a [Colab](https://colab.research.google.com/drive/1VKd1gAB-6AIdMzBCG0J-U7h9vwsiKnHp) Demo for inference. +- [2024/04/13] Update scripts for single-subject, cross-subject training, and new subject adaptation. - [2024/04/12] Inference and pretrained model available. Training code coming up soon. - [2024/04/11] BrainHub is available. - [2024/03/15] Both project and arXiv are available. @@ -145,11 +147,12 @@ do done ``` -We also provide baseline results associated with BrainHub, including the captioning results from [SDRecon](https://github.com/yu-takagi/StableDiffusionReconstruction), [BrainCap](https://arxiv.org/abs/2305.11560), and [OneLLM](https://onellm.csuhan.com/), as well as the captioning and grounding results from [UMBRAE](https://weihaox.github.io/UMBRAE/). +We also provide baseline results associated with [BrainHub](https://github.com/weihaox/BrainHub/tree/main/caption/comparison), including the captioning results from [SDRecon](https://github.com/yu-takagi/StableDiffusionReconstruction), [BrainCap](https://arxiv.org/abs/2305.11560), and [OneLLM](https://onellm.csuhan.com/), as well as the captioning and grounding results from [UMBRAE](https://weihaox.github.io/UMBRAE/). ## TODO - [x] Release inference scripts and pretrained checkpoints. -- [x] Update training scripts +- [x] Update training scripts. +- [x] Provide online demo. - [ ] Train on all 8 subjects in NSD. - [ ] Support other MLLMs such as NExT-Chat, CogVLM, Genixer diff --git a/umbrae/download_checkpoint.sh b/umbrae/download_checkpoint.sh index 29287e9..72d9a99 100644 --- a/umbrae/download_checkpoint.sh +++ b/umbrae/download_checkpoint.sh @@ -7,4 +7,4 @@ # @Desc : download Checkpoints from Hugging Face # ------------------------------------------------------------------ -python -c 'from huggingface_hub import snapshot_download; snapshot_download(repo_id="weihaox/brainx", repo_type="dataset", local_dir="./", , ignore_patterns=["all_images.pt", ".gitattributes"])' \ No newline at end of file +python -c 'from huggingface_hub import snapshot_download; snapshot_download(repo_id="weihaox/brainx", repo_type="dataset", local_dir="./", ignore_patterns=["all_images.pt", ".gitattributes"])' \ No newline at end of file diff --git a/umbrae/environment.yaml b/umbrae/environment.yaml new file mode 100644 index 0000000..5deef31 --- /dev/null +++ b/umbrae/environment.yaml @@ -0,0 +1,21 @@ +name: brainx +channels: + - pytorch + - nvidia + - conda-forge + - fvcore + - iopath + - bottler + - defaults +dependencies: + - python=3.8 + - pytorch-cuda=11.6 + - pytorch=1.13.0 + - nvidiacub + - torchvision + - fvcore + - iopath + - pyembree + - cupy + - cython + - pip \ No newline at end of file diff --git a/umbrae/playground.ipynb b/umbrae/playground.ipynb new file mode 100644 index 0000000..f4621c3 --- /dev/null +++ b/umbrae/playground.ipynb @@ -0,0 +1,1307 @@ +{ + "nbformat": 4, + "nbformat_minor": 0, + "metadata": { + "colab": { + "provenance": [], + "machine_shape": "hm", + "gpuType": "T4" + }, + "kernelspec": { + "name": "python3", + "display_name": "Python 3" + }, + "language_info": { + "name": "python" + }, + "accelerator": "GPU" + }, + "cells": [ + { + "cell_type": "markdown", + "source": [ + "### Checking system requirements" + ], + "metadata": { + "id": "yb3UzidIkQpX" + } + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "CfGCySddjy7J", + "outputId": "a673f4e4-52bf-4cb4-ab1c-32f857bd772f" + }, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "Tue Apr 16 16:45:58 2024 \n", + "+---------------------------------------------------------------------------------------+\n", + "| NVIDIA-SMI 535.104.05 Driver Version: 535.104.05 CUDA Version: 12.2 |\n", + "|-----------------------------------------+----------------------+----------------------+\n", + "| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |\n", + "| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |\n", + "| | | MIG M. |\n", + "|=========================================+======================+======================|\n", + "| 0 Tesla T4 Off | 00000000:00:04.0 Off | 0 |\n", + "| N/A 47C P8 10W / 70W | 0MiB / 15360MiB | 0% Default |\n", + "| | | N/A |\n", + "+-----------------------------------------+----------------------+----------------------+\n", + " \n", + "+---------------------------------------------------------------------------------------+\n", + "| Processes: |\n", + "| GPU GI CI PID Type Process name GPU Memory |\n", + "| ID ID Usage |\n", + "|=======================================================================================|\n", + "| No running processes found |\n", + "+---------------------------------------------------------------------------------------+\n" + ] + } + ], + "source": [ + "# connected to NVIDIA drivers with CUDA.\n", + "!nvidia-smi" + ] + }, + { + "cell_type": "code", + "source": [ + "# Checking OS version\n", + "!cat /etc/os-release | head -n2" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "YDlPOLd4kWic", + "outputId": "d9f87251-d0fc-4f40-99e4-d40cb089f4c6" + }, + "execution_count": null, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "PRETTY_NAME=\"Ubuntu 22.04.3 LTS\"\n", + "NAME=\"Ubuntu\"\n" + ] + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "### Installing prerequisites" + ], + "metadata": { + "id": "-Fbs-SwgkdUb" + } + }, + { + "cell_type": "code", + "source": [ + "# clone repository\n", + "\n", + "!git clone https://github.com/weihaox/UMBRAE\n", + "!git clone https://github.com/weihaox/BrainHub" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "v5gYKZLrkix2", + "outputId": "bac84965-fd3c-4bfb-9402-786bcc56f8e9" + }, + "execution_count": null, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "Cloning into 'UMBRAE'...\n", + "remote: Enumerating objects: 66, done.\u001b[K\n", + "remote: Counting objects: 100% (66/66), done.\u001b[K\n", + "remote: Compressing objects: 100% (55/55), done.\u001b[K\n", + "remote: Total 66 (delta 11), reused 63 (delta 8), pack-reused 0\u001b[K\n", + "Receiving objects: 100% (66/66), 29.70 MiB | 57.60 MiB/s, done.\n", + "Resolving deltas: 100% (11/11), done.\n", + "Cloning into 'BrainHub'...\n", + "remote: Enumerating objects: 44, done.\u001b[K\n", + "remote: Counting objects: 100% (44/44), done.\u001b[K\n", + "remote: Compressing objects: 100% (31/31), done.\u001b[K\n", + "remote: Total 44 (delta 9), reused 44 (delta 9), pack-reused 0\u001b[K\n", + "Receiving objects: 100% (44/44), 504.58 KiB | 8.55 MiB/s, done.\n", + "Resolving deltas: 100% (9/9), done.\n" + ] + } + ] + }, + { + "cell_type": "code", + "source": [ + "# install mamba and update base\n", + "\n", + "%%shell\n", + "curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh\n", + "chmod +x Mambaforge-Linux-x86_64.sh\n", + "bash Mambaforge-Linux-x86_64.sh -b -f -p /usr/local\n", + "mamba config --env --set always_yes true\n", + "rm Mambaforge-Linux-x86_64.sh\n", + "mamba update -n base -c defaults conda -y" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "OqAaPf5hk2nq", + "outputId": "ff43241a-ae1d-4b0e-d1d0-81c0b990f21d" + }, + "execution_count": null, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + " % Total % Received % Xferd Average Speed Time Time Time Current\n", + " Dload Upload Total Spent Left Speed\n", + "\r 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0\r 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0\n", + " 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0\n", + "100 80.5M 100 80.5M 0 0 62.4M 0 0:00:01 0:00:01 --:--:-- 77.6M\n", + "PREFIX=/usr/local\n", + "Unpacking payload ...\n", + 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libuuid-2.38.1-h0b41bf4_0.conda\n", + "Extracting libxcrypt-4.4.36-hd590300_1.conda\n", + "Extracting libzlib-1.2.13-hd590300_5.conda\n", + "Extracting lz4-c-1.9.4-hcb278e6_0.conda\n", + "Extracting lzo-2.10-h516909a_1000.tar.bz2\n", + "Extracting ncurses-6.4.20240210-h59595ed_0.conda\n", + "Extracting openssl-3.2.1-hd590300_1.conda\n", + "Extracting reproc-14.2.4.post0-hd590300_1.conda\n", + "Extracting xz-5.2.6-h166bdaf_0.tar.bz2\n", + "Extracting yaml-cpp-0.8.0-h59595ed_0.conda\n", + "Extracting libedit-3.1.20191231-he28a2e2_2.tar.bz2\n", + "Extracting libnghttp2-1.58.0-h47da74e_1.conda\n", + "Extracting libsolv-0.7.28-hfc55251_0.conda\n", + "Extracting libsqlite-3.45.2-h2797004_0.conda\n", + "Extracting libssh2-1.11.0-h0841786_0.conda\n", + "Extracting libxml2-2.12.6-h232c23b_0.conda\n", + "Extracting readline-8.2-h8228510_1.conda\n", + "Extracting reproc-cpp-14.2.4.post0-h59595ed_1.conda\n", + "Extracting tk-8.6.13-noxft_h4845f30_101.conda\n", + "Extracting zstd-1.5.5-hfc55251_0.conda\n", + "Extracting krb5-1.21.2-h659d440_0.conda\n", + "Extracting libarchive-3.7.2-h2aa1ff5_1.conda\n", + "Extracting python-3.10.14-hd12c33a_0_cpython.conda\n", + "Extracting libcurl-8.6.0-hca28451_0.conda\n", + "Extracting menuinst-2.0.2-py310hff52083_0.conda\n", + "Extracting archspec-0.2.3-pyhd8ed1ab_0.conda\n", + "Extracting boltons-23.1.1-pyhd8ed1ab_0.conda\n", + "Extracting brotli-python-1.1.0-py310hc6cd4ac_1.conda\n", + "Extracting certifi-2024.2.2-pyhd8ed1ab_0.conda\n", + "Extracting charset-normalizer-3.3.2-pyhd8ed1ab_0.conda\n", + "Extracting colorama-0.4.6-pyhd8ed1ab_0.tar.bz2\n", + "Extracting distro-1.9.0-pyhd8ed1ab_0.conda\n", + "Extracting idna-3.6-pyhd8ed1ab_0.conda\n", + "Extracting jsonpointer-2.4-py310hff52083_3.conda\n", + "Extracting libmamba-1.5.7-had39da4_0.conda\n", + "Extracting packaging-24.0-pyhd8ed1ab_0.conda\n", + "Extracting platformdirs-4.2.0-pyhd8ed1ab_0.conda\n", + "Extracting pluggy-1.4.0-pyhd8ed1ab_0.conda\n", + "Extracting pycosat-0.6.6-py310h2372a71_0.conda\n", + "Extracting pycparser-2.21-pyhd8ed1ab_0.tar.bz2\n", + "Extracting pysocks-1.7.1-pyha2e5f31_6.tar.bz2\n", + "Extracting ruamel.yaml.clib-0.2.8-py310h2372a71_0.conda\n", + "Extracting setuptools-69.2.0-pyhd8ed1ab_0.conda\n", + "Extracting truststore-0.8.0-pyhd8ed1ab_0.conda\n", + "Extracting wheel-0.43.0-pyhd8ed1ab_0.conda\n", + "Extracting cffi-1.16.0-py310h2fee648_0.conda\n", + "Extracting jsonpatch-1.33-pyhd8ed1ab_0.conda\n", + "Extracting libmambapy-1.5.7-py310h39ff949_0.conda\n", + "Extracting pip-24.0-pyhd8ed1ab_0.conda\n", + "Extracting ruamel.yaml-0.18.6-py310h2372a71_0.conda\n", + "Extracting tqdm-4.66.2-pyhd8ed1ab_0.conda\n", + "Extracting urllib3-2.2.1-pyhd8ed1ab_0.conda\n", + "Extracting requests-2.31.0-pyhd8ed1ab_0.conda\n", + "Extracting zstandard-0.22.0-py310h1275a96_0.conda\n", + "Extracting conda-package-streaming-0.9.0-pyhd8ed1ab_0.conda\n", + "Extracting conda-package-handling-2.2.0-pyh38be061_0.conda\n", + "Extracting conda-24.1.2-py310hff52083_0.conda\n", + "Extracting conda-libmamba-solver-24.1.0-pyhd8ed1ab_0.conda\n", + "Extracting mamba-1.5.7-py310h51d5547_0.conda\n", + "\n", + "Installing base environment...\n", + "\n", + "\n", + " __\n", + " __ ______ ___ ____ _____ ___ / /_ ____ _\n", + " / / / / __ `__ \\/ __ `/ __ `__ \\/ __ \\/ __ `/\n", + " / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /\n", + " / .___/_/ /_/ /_/\\__,_/_/ /_/ /_/_.___/\\__,_/\n", + " /_/\n", + "\n", + "Transaction\n", + "\n", + " Prefix: /usr/local\n", + "\n", + " Updating specs:\n", + "\n", + " - conda-forge/linux-64::_libgcc_mutex==0.1=conda_forge[md5=d7c89558ba9fa0495403155b64376d81]\n", + " - conda-forge/linux-64::ca-certificates==2024.2.2=hbcca054_0[md5=2f4327a1cbe7f022401b236e915a5fef]\n", + " - conda-forge/linux-64::ld_impl_linux-64==2.40=h41732ed_0[md5=7aca3059a1729aa76c597603f10b0dd3]\n", + " - conda-forge/linux-64::libstdcxx-ng==13.2.0=h7e041cc_5[md5=f6f6600d18a4047b54f803cf708b868a]\n", + " - conda-forge/noarch::pybind11-abi==4=hd8ed1ab_3[md5=878f923dd6acc8aeb47a75da6c4098be]\n", + " - conda-forge/linux-64::python_abi==3.10=4_cp310[md5=26322ec5d7712c3ded99dd656142b8ce]\n", + " - conda-forge/noarch::tzdata==2024a=h0c530f3_0[md5=161081fc7cec0bfda0d86d7cb595f8d8]\n", + " - conda-forge/linux-64::libgomp==13.2.0=h807b86a_5[md5=d211c42b9ce49aee3734fdc828731689]\n", + " - conda-forge/linux-64::_openmp_mutex==4.5=2_gnu[md5=73aaf86a425cc6e73fcf236a5a46396d]\n", + " - conda-forge/linux-64::libgcc-ng==13.2.0=h807b86a_5[md5=d4ff227c46917d3b4565302a2bbb276b]\n", + " - conda-forge/linux-64::bzip2==1.0.8=hd590300_5[md5=69b8b6202a07720f448be700e300ccf4]\n", + " - conda-forge/linux-64::c-ares==1.27.0=hd590300_0[md5=f6afff0e9ee08d2f1b897881a4f38cdb]\n", + " - conda-forge/linux-64::fmt==10.2.1=h00ab1b0_0[md5=35ef8bc24bd34074ebae3c943d551728]\n", + " - conda-forge/linux-64::icu==73.2=h59595ed_0[md5=cc47e1facc155f91abd89b11e48e72ff]\n", + " - conda-forge/linux-64::keyutils==1.6.1=h166bdaf_0[md5=30186d27e2c9fa62b45fb1476b7200e3]\n", + " - conda-forge/linux-64::libev==4.33=hd590300_2[md5=172bf1cd1ff8629f2b1179945ed45055]\n", + " - conda-forge/linux-64::libffi==3.4.2=h7f98852_5[md5=d645c6d2ac96843a2bfaccd2d62b3ac3]\n", + " - conda-forge/linux-64::libiconv==1.17=hd590300_2[md5=d66573916ffcf376178462f1b61c941e]\n", + " - conda-forge/linux-64::libnsl==2.0.1=hd590300_0[md5=30fd6e37fe21f86f4bd26d6ee73eeec7]\n", + " - conda-forge/linux-64::libuuid==2.38.1=h0b41bf4_0[md5=40b61aab5c7ba9ff276c41cfffe6b80b]\n", + " - conda-forge/linux-64::libxcrypt==4.4.36=hd590300_1[md5=5aa797f8787fe7a17d1b0821485b5adc]\n", + " - conda-forge/linux-64::libzlib==1.2.13=hd590300_5[md5=f36c115f1ee199da648e0597ec2047ad]\n", + " - conda-forge/linux-64::lz4-c==1.9.4=hcb278e6_0[md5=318b08df404f9c9be5712aaa5a6f0bb0]\n", + " - conda-forge/linux-64::lzo==2.10=h516909a_1000[md5=bb14fcb13341b81d5eb386423b9d2bac]\n", + " - conda-forge/linux-64::ncurses==6.4.20240210=h59595ed_0[md5=97da8860a0da5413c7c98a3b3838a645]\n", + " - conda-forge/linux-64::openssl==3.2.1=hd590300_1[md5=9d731343cff6ee2e5a25c4a091bf8e2a]\n", + " - conda-forge/linux-64::reproc==14.2.4.post0=hd590300_1[md5=82ca53502dfd5a64a80dee76dae14685]\n", + " - conda-forge/linux-64::xz==5.2.6=h166bdaf_0[md5=2161070d867d1b1204ea749c8eec4ef0]\n", + " - conda-forge/linux-64::yaml-cpp==0.8.0=h59595ed_0[md5=965eaacd7c18eb8361fd12bb9e7a57d7]\n", + " - conda-forge/linux-64::libedit==3.1.20191231=he28a2e2_2[md5=4d331e44109e3f0e19b4cb8f9b82f3e1]\n", + " - conda-forge/linux-64::libnghttp2==1.58.0=h47da74e_1[md5=700ac6ea6d53d5510591c4344d5c989a]\n", + " - conda-forge/linux-64::libsolv==0.7.28=hfc55251_0[md5=66d4f5d8256542d9ebfa341d690c5e03]\n", + " - conda-forge/linux-64::libsqlite==3.45.2=h2797004_0[md5=866983a220e27a80cb75e85cb30466a1]\n", + " - conda-forge/linux-64::libssh2==1.11.0=h0841786_0[md5=1f5a58e686b13bcfde88b93f547d23fe]\n", + " - conda-forge/linux-64::libxml2==2.12.6=h232c23b_0[md5=d86653ff5ccb88bf7f13833fdd8789e0]\n", + " - conda-forge/linux-64::readline==8.2=h8228510_1[md5=47d31b792659ce70f470b5c82fdfb7a4]\n", + " - conda-forge/linux-64::reproc-cpp==14.2.4.post0=h59595ed_1[md5=715e1d720ec1a03715bebd237972fca5]\n", + " - conda-forge/linux-64::tk==8.6.13=noxft_h4845f30_101[md5=d453b98d9c83e71da0741bb0ff4d76bc]\n", + " - conda-forge/linux-64::zstd==1.5.5=hfc55251_0[md5=04b88013080254850d6c01ed54810589]\n", + " - conda-forge/linux-64::krb5==1.21.2=h659d440_0[md5=cd95826dbd331ed1be26bdf401432844]\n", + " - conda-forge/linux-64::libarchive==3.7.2=h2aa1ff5_1[md5=3bf887827d1968275978361a6e405e4f]\n", + " - conda-forge/linux-64::python==3.10.14=hd12c33a_0_cpython[md5=2b4ba962994e8bd4be9ff5b64b75aff2]\n", + " - conda-forge/linux-64::libcurl==8.6.0=hca28451_0[md5=704739398d858872cb91610f49f0ef29]\n", + " - conda-forge/linux-64::menuinst==2.0.2=py310hff52083_0[md5=4837faab0d3e665df57fef662148c6a3]\n", + " - conda-forge/noarch::archspec==0.2.3=pyhd8ed1ab_0[md5=192278292e20704f663b9c766909d67b]\n", + " - conda-forge/noarch::boltons==23.1.1=pyhd8ed1ab_0[md5=56febe65315cc388a5d20adf2b39a74d]\n", + " - conda-forge/linux-64::brotli-python==1.1.0=py310hc6cd4ac_1[md5=1f95722c94f00b69af69a066c7433714]\n", + " - conda-forge/noarch::certifi==2024.2.2=pyhd8ed1ab_0[md5=0876280e409658fc6f9e75d035960333]\n", + " - conda-forge/noarch::charset-normalizer==3.3.2=pyhd8ed1ab_0[md5=7f4a9e3fcff3f6356ae99244a014da6a]\n", + " - conda-forge/noarch::colorama==0.4.6=pyhd8ed1ab_0[md5=3faab06a954c2a04039983f2c4a50d99]\n", + " - conda-forge/noarch::distro==1.9.0=pyhd8ed1ab_0[md5=bbdb409974cd6cb30071b1d978302726]\n", + " - conda-forge/noarch::idna==3.6=pyhd8ed1ab_0[md5=1a76f09108576397c41c0b0c5bd84134]\n", + " - conda-forge/linux-64::jsonpointer==2.4=py310hff52083_3[md5=08ec1463dbc5c806a32fc431874032ca]\n", + " - conda-forge/linux-64::libmamba==1.5.7=had39da4_0[md5=9fff450354fbcd1510ef178730732241]\n", + " - conda-forge/noarch::packaging==24.0=pyhd8ed1ab_0[md5=248f521b64ce055e7feae3105e7abeb8]\n", + " - conda-forge/noarch::platformdirs==4.2.0=pyhd8ed1ab_0[md5=a0bc3eec34b0fab84be6b2da94e98e20]\n", + " - conda-forge/noarch::pluggy==1.4.0=pyhd8ed1ab_0[md5=139e9feb65187e916162917bb2484976]\n", + " - conda-forge/linux-64::pycosat==0.6.6=py310h2372a71_0[md5=0adaac9a86d59adae2bc86b3cdef2df1]\n", + " - conda-forge/noarch::pycparser==2.21=pyhd8ed1ab_0[md5=076becd9e05608f8dc72757d5f3a91ff]\n", + " - conda-forge/noarch::pysocks==1.7.1=pyha2e5f31_6[md5=2a7de29fb590ca14b5243c4c812c8025]\n", + " - conda-forge/linux-64::ruamel.yaml.clib==0.2.8=py310h2372a71_0[md5=dcf6d2535586c77b31425ed835610c54]\n", + " - conda-forge/noarch::setuptools==69.2.0=pyhd8ed1ab_0[md5=da214ecd521a720a9d521c68047682dc]\n", + " - conda-forge/noarch::truststore==0.8.0=pyhd8ed1ab_0[md5=08316d001eca8854392cf2837828ea11]\n", + " - conda-forge/noarch::wheel==0.43.0=pyhd8ed1ab_0[md5=6e43a94e0ee67523b5e781f0faba5c45]\n", + " - conda-forge/linux-64::cffi==1.16.0=py310h2fee648_0[md5=45846a970e71ac98fd327da5d40a0a2c]\n", + " - conda-forge/noarch::jsonpatch==1.33=pyhd8ed1ab_0[md5=bfdb7c5c6ad1077c82a69a8642c87aff]\n", + " - conda-forge/linux-64::libmambapy==1.5.7=py310h39ff949_0[md5=58d84efb37d517c64f4e48f75fd6180d]\n", + " - conda-forge/noarch::pip==24.0=pyhd8ed1ab_0[md5=f586ac1e56c8638b64f9c8122a7b8a67]\n", + " - conda-forge/linux-64::ruamel.yaml==0.18.6=py310h2372a71_0[md5=50b7d9b39099cdbabf65bf27df73a793]\n", + " - conda-forge/noarch::tqdm==4.66.2=pyhd8ed1ab_0[md5=2b8dfb969f984497f3f98409a9545776]\n", + " - conda-forge/noarch::urllib3==2.2.1=pyhd8ed1ab_0[md5=08807a87fa7af10754d46f63b368e016]\n", + " - conda-forge/noarch::requests==2.31.0=pyhd8ed1ab_0[md5=a30144e4156cdbb236f99ebb49828f8b]\n", + " - conda-forge/linux-64::zstandard==0.22.0=py310h1275a96_0[md5=54698ba13cd3494547b289cd86a2176a]\n", + " - conda-forge/noarch::conda-package-streaming==0.9.0=pyhd8ed1ab_0[md5=38253361efb303deead3eab39ae9269b]\n", + " - conda-forge/noarch::conda-package-handling==2.2.0=pyh38be061_0[md5=8a3ae7f6318376aa08ea753367bb7dd6]\n", + " - conda-forge/linux-64::conda==24.1.2=py310hff52083_0[md5=d7a8a166cf89ed19a7d3ee41b71a5d6f]\n", + " - conda-forge/noarch::conda-libmamba-solver==24.1.0=pyhd8ed1ab_0[md5=304dc78ad6e52e0fd663df1d484c1531]\n", + " - conda-forge/linux-64::mamba==1.5.7=py310h51d5547_0[md5=5977cafef2904d1588d0c23b94846f2c]\n", + "\n", + "\n", + " Package Version Build Channel Size\n", + "───────────────────────────────────────────────────────────────────────────────────────\n", + " Install:\n", + "───────────────────────────────────────────────────────────────────────────────────────\n", + "\n", + " \u001b[32m+ _libgcc_mutex \u001b[0m 0.1 conda_forge conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ _openmp_mutex \u001b[0m 4.5 2_gnu conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ archspec \u001b[0m 0.2.3 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ boltons \u001b[0m 23.1.1 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ brotli-python \u001b[0m 1.1.0 py310hc6cd4ac_1 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ bzip2 \u001b[0m 1.0.8 hd590300_5 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ c-ares \u001b[0m 1.27.0 hd590300_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ ca-certificates \u001b[0m 2024.2.2 hbcca054_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ certifi \u001b[0m 2024.2.2 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ cffi \u001b[0m 1.16.0 py310h2fee648_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ charset-normalizer \u001b[0m 3.3.2 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ colorama \u001b[0m 0.4.6 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ conda \u001b[0m 24.1.2 py310hff52083_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ conda-libmamba-solver \u001b[0m 24.1.0 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ conda-package-handling \u001b[0m 2.2.0 pyh38be061_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ conda-package-streaming\u001b[0m 0.9.0 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ distro \u001b[0m 1.9.0 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ fmt \u001b[0m 10.2.1 h00ab1b0_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ icu \u001b[0m 73.2 h59595ed_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ idna \u001b[0m 3.6 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ jsonpatch \u001b[0m 1.33 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ jsonpointer \u001b[0m 2.4 py310hff52083_3 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ keyutils \u001b[0m 1.6.1 h166bdaf_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ krb5 \u001b[0m 1.21.2 h659d440_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ ld_impl_linux-64 \u001b[0m 2.40 h41732ed_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libarchive \u001b[0m 3.7.2 h2aa1ff5_1 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libcurl \u001b[0m 8.6.0 hca28451_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libedit \u001b[0m 3.1.20191231 he28a2e2_2 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libev \u001b[0m 4.33 hd590300_2 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libffi \u001b[0m 3.4.2 h7f98852_5 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libgcc-ng \u001b[0m 13.2.0 h807b86a_5 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libgomp \u001b[0m 13.2.0 h807b86a_5 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libiconv \u001b[0m 1.17 hd590300_2 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libmamba \u001b[0m 1.5.7 had39da4_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libmambapy \u001b[0m 1.5.7 py310h39ff949_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libnghttp2 \u001b[0m 1.58.0 h47da74e_1 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libnsl \u001b[0m 2.0.1 hd590300_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libsolv \u001b[0m 0.7.28 hfc55251_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libsqlite \u001b[0m 3.45.2 h2797004_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libssh2 \u001b[0m 1.11.0 h0841786_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libstdcxx-ng \u001b[0m 13.2.0 h7e041cc_5 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libuuid \u001b[0m 2.38.1 h0b41bf4_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libxcrypt \u001b[0m 4.4.36 hd590300_1 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libxml2 \u001b[0m 2.12.6 h232c23b_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ libzlib \u001b[0m 1.2.13 hd590300_5 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ lz4-c \u001b[0m 1.9.4 hcb278e6_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ lzo \u001b[0m 2.10 h516909a_1000 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ mamba \u001b[0m 1.5.7 py310h51d5547_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ menuinst \u001b[0m 2.0.2 py310hff52083_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ ncurses \u001b[0m 6.4.20240210 h59595ed_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ openssl \u001b[0m 3.2.1 hd590300_1 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ packaging \u001b[0m 24.0 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ pip \u001b[0m 24.0 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ platformdirs \u001b[0m 4.2.0 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ pluggy \u001b[0m 1.4.0 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ pybind11-abi \u001b[0m 4 hd8ed1ab_3 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ pycosat \u001b[0m 0.6.6 py310h2372a71_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ pycparser \u001b[0m 2.21 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ pysocks \u001b[0m 1.7.1 pyha2e5f31_6 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ python \u001b[0m 3.10.14 hd12c33a_0_cpython conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ python_abi \u001b[0m 3.10 4_cp310 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ readline \u001b[0m 8.2 h8228510_1 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ reproc \u001b[0m 14.2.4.post0 hd590300_1 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ reproc-cpp \u001b[0m 14.2.4.post0 h59595ed_1 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ requests \u001b[0m 2.31.0 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ ruamel.yaml \u001b[0m 0.18.6 py310h2372a71_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ ruamel.yaml.clib \u001b[0m 0.2.8 py310h2372a71_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ setuptools \u001b[0m 69.2.0 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ tk \u001b[0m 8.6.13 noxft_h4845f30_101 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ tqdm \u001b[0m 4.66.2 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ truststore \u001b[0m 0.8.0 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ tzdata \u001b[0m 2024a h0c530f3_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ urllib3 \u001b[0m 2.2.1 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ wheel \u001b[0m 0.43.0 pyhd8ed1ab_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ xz \u001b[0m 5.2.6 h166bdaf_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ yaml-cpp \u001b[0m 0.8.0 h59595ed_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ zstandard \u001b[0m 0.22.0 py310h1275a96_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ zstd \u001b[0m 1.5.5 hfc55251_0 conda-forge\u001b[32m Cached\u001b[0m\n", + "\n", + " Summary:\n", + "\n", + " Install: 78 packages\n", + "\n", + " Total download: 0 B\n", + "\n", + "───────────────────────────────────────────────────────────────────────────────────────\n", + "\n", + "\n", + "\n", + "Transaction starting\n", + "\u001b[?25l\u001b[2K\u001b[0G\u001b[?25hLinking _libgcc_mutex-0.1-conda_forge\n", + "Linking ca-certificates-2024.2.2-hbcca054_0\n", + "Linking ld_impl_linux-64-2.40-h41732ed_0\n", + "Linking libstdcxx-ng-13.2.0-h7e041cc_5\n", + "Linking pybind11-abi-4-hd8ed1ab_3\n", + "Linking python_abi-3.10-4_cp310\n", + "Linking tzdata-2024a-h0c530f3_0\n", + "Linking libgomp-13.2.0-h807b86a_5\n", + "Linking _openmp_mutex-4.5-2_gnu\n", + "Linking libgcc-ng-13.2.0-h807b86a_5\n", + "Linking 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"Linking colorama-0.4.6-pyhd8ed1ab_0\n", + "Linking distro-1.9.0-pyhd8ed1ab_0\n", + "Linking idna-3.6-pyhd8ed1ab_0\n", + "Linking jsonpointer-2.4-py310hff52083_3\n", + "Linking libmamba-1.5.7-had39da4_0\n", + "Linking packaging-24.0-pyhd8ed1ab_0\n", + "Linking platformdirs-4.2.0-pyhd8ed1ab_0\n", + "Linking pluggy-1.4.0-pyhd8ed1ab_0\n", + "Linking pycosat-0.6.6-py310h2372a71_0\n", + "Linking pycparser-2.21-pyhd8ed1ab_0\n", + "Linking pysocks-1.7.1-pyha2e5f31_6\n", + "Linking ruamel.yaml.clib-0.2.8-py310h2372a71_0\n", + "Linking setuptools-69.2.0-pyhd8ed1ab_0\n", + "Linking truststore-0.8.0-pyhd8ed1ab_0\n", + "Linking wheel-0.43.0-pyhd8ed1ab_0\n", + "\u001b[33m\u001b[1mwarning libmamba\u001b[m [wheel-0.43.0-pyhd8ed1ab_0] The following files were already present in the environment:\n", + " - bin/wheel\n", + "Linking cffi-1.16.0-py310h2fee648_0\n", + "Linking jsonpatch-1.33-pyhd8ed1ab_0\n", + "Linking libmambapy-1.5.7-py310h39ff949_0\n", + "Linking pip-24.0-pyhd8ed1ab_0\n", + "\u001b[33m\u001b[1mwarning libmamba\u001b[m [pip-24.0-pyhd8ed1ab_0] The following files were already present in the environment:\n", + " - bin/pip\n", + " - bin/pip3\n", + "Linking ruamel.yaml-0.18.6-py310h2372a71_0\n", + "Linking tqdm-4.66.2-pyhd8ed1ab_0\n", + "\u001b[33m\u001b[1mwarning libmamba\u001b[m [tqdm-4.66.2-pyhd8ed1ab_0] The following files were already present in the environment:\n", + " - bin/tqdm\n", + "Linking urllib3-2.2.1-pyhd8ed1ab_0\n", + "Linking requests-2.31.0-pyhd8ed1ab_0\n", + "Linking zstandard-0.22.0-py310h1275a96_0\n", + "Linking conda-package-streaming-0.9.0-pyhd8ed1ab_0\n", + "Linking conda-package-handling-2.2.0-pyh38be061_0\n", + "Linking conda-24.1.2-py310hff52083_0\n", + "Linking conda-libmamba-solver-24.1.0-pyhd8ed1ab_0\n", + "Linking mamba-1.5.7-py310h51d5547_0\n", + "Transaction finished\n", + "installation finished.\n", + "WARNING:\n", + " You currently have a PYTHONPATH environment variable set. This may cause\n", + " unexpected behavior when running the Python interpreter in Mambaforge.\n", + " For best results, please verify that your PYTHONPATH only points to\n", + " directories of packages that are compatible with the Python interpreter\n", + " in Mambaforge: /usr/local\n", + "Currently, only install, create, list, search, run, info, clean, remove, update, repoquery, activate and deactivate are supported through mamba.\n", + "\n", + "Looking for: ['conda']\n", + "\n", + "\u001b[?25l\u001b[2K\u001b[0G[+] 0.0s\n", + "\u001b[2K\u001b[1A\u001b[2K\u001b[0G[+] 0.1s\n", + "pkgs/main/linux-64.. ⣾ \u001b[2K\u001b[1A\u001b[2K\u001b[0Gpkgs/main/linux-64 (check zst) \n", + "\u001b[?25h\u001b[?25l\u001b[2K\u001b[0G[+] 0.0s\n", + "pkgs/main/noarch (.. ⣾ \u001b[2K\u001b[1A\u001b[2K\u001b[0Gpkgs/main/noarch (check zst) \n", + "\u001b[?25h\u001b[?25l\u001b[2K\u001b[0G[+] 0.0s\n", + "pkgs/r/linux-64 (c.. ⣾ \u001b[2K\u001b[1A\u001b[2K\u001b[0Gpkgs/r/linux-64 (check zst) \n", + 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specs:\n", + "\n", + " - conda\n", + " - ca-certificates\n", + " - certifi\n", + " - openssl\n", + "\n", + "\n", + " Package Version Build Channel Size\n", + "─────────────────────────────────────────────────────────────────────────\n", + " Upgrade:\n", + "─────────────────────────────────────────────────────────────────────────\n", + "\n", + " \u001b[31m- ca-certificates\u001b[0m 2024.2.2 hbcca054_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ ca-certificates\u001b[0m 2024.3.11 h06a4308_0 pkgs/main 130kB\n", + " \u001b[31m- conda \u001b[0m 24.1.2 py310hff52083_0 conda-forge\u001b[32m Cached\u001b[0m\n", + " \u001b[32m+ conda \u001b[0m 24.3.0 py310h06a4308_0 pkgs/main 980kB\n", + "\n", + " Summary:\n", + "\n", + " Upgrade: 2 packages\n", + "\n", + " Total download: 1MB\n", + "\n", + "─────────────────────────────────────────────────────────────────────────\n", + "\n", + "\n", + "\u001b[?25l\u001b[2K\u001b[0G[+] 0.0s\n", + "Downloading 0%\n", + "Extracting 0%\u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gca-certificates 130.4kB @ 1.6MB/s 0.1s\n", + "[+] 0.1s\n", + "Downloading (1) 12%\n", + "Extracting (1) ⣾ \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0Gconda 979.9kB @ 7.5MB/s 0.1s\n", + "[+] 0.2s\n", + "Downloading 100%\n", + "Extracting (1) ⣾ \u001b[2K\u001b[1A\u001b[2K\u001b[1A\u001b[2K\u001b[0G\u001b[?25h\n", + "Downloading and Extracting Packages:\n", + "\n", + "Preparing transaction: - \b\bdone\n", + "Verifying transaction: | \b\bdone\n", + "Executing transaction: - \b\bdone\n" + ] + }, + { + "output_type": "execute_result", + "data": { + "text/plain": [] + }, + "metadata": {}, + "execution_count": 4 + } + ] + }, + { + "cell_type": "code", + "source": [ + "%%shell\n", + "cd UMBRAE/umbrae\n", + "mamba env create -f environment.yaml > /dev/null\n", + "mamba init bash\n", + "source /root/.bashrc\n", + "source activate brainx" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "YzzfoicMkwoC", + "outputId": "a0ce28ea-d459-4a94-e52f-692222d4ac9c" + }, + "execution_count": null, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "no change /usr/local/condabin/conda\n", + "no change /usr/local/bin/conda\n", + "no change /usr/local/bin/conda-env\n", + "no change /usr/local/bin/activate\n", + "no change /usr/local/bin/deactivate\n", + "no change /usr/local/etc/profile.d/conda.sh\n", + "no change /usr/local/etc/fish/conf.d/conda.fish\n", + "no change /usr/local/shell/condabin/Conda.psm1\n", + "no change /usr/local/shell/condabin/conda-hook.ps1\n", + "no change /usr/local/lib/python3.10/site-packages/xontrib/conda.xsh\n", + "no change /usr/local/etc/profile.d/conda.csh\n", + "modified /root/.bashrc\n", + "\n", + "==> For changes to take effect, close and re-open your current shell. <==\n", + "\n", + "Added mamba to /root/.bashrc\n", + "\n", + "==> For changes to take effect, close and re-open your current shell. <==\n", + "\n", + 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"Installing collected packages: wcwidth, SentencePiece, pytz, pydub, ffmpy, braceexpand, addict, zipp, xxhash, websockets, webdataset, tzdata, toolz, tomlkit, tomli, threadpoolctl, tensorboard-data-server, sniffio, six, shellingham, semantic-version, scipy, safetensors, ruff, rpds-py, regex, python-multipart, pyparsing, pygments, pydantic-core, pyasn1, pyarrow-hotfix, pyarrow, psutil, protobuf, platformdirs, pkgutil-resolve-name, packaging, orjson, opencv-python, oauthlib, multidict, mdurl, markupsafe, llvmlite, kornia-rs, kiwisolver, joblib, h11, grpcio, fsspec, frozenlist, fonttools, filelock, exceptiongroup, einops, dill, cycler, contourpy, click, cachetools, attrs, async-timeout, annotated-types, aiofiles, absl-py, yarl, werkzeug, uvicorn, scikit-learn, rsa, requests-oauthlib, referencing, python-dateutil, pydantic, pyasn1-modules, nltk, multiprocess, markdown-it-py, kornia, jinja2, importlib-resources, importlib-metadata, huggingface-hub, httpcore, einops_exts, bitsandbytes, anyio, aiosignal, accelerate, yapf, tokenizers, starlette, rich, pandas, numba, matplotlib, markdown, jsonschema-specifications, httpx, google-auth, aiohttp, typer, transformers, pynndescent, pycocotools, mmengine, jsonschema, gradio-client, google-auth-oauthlib, fastapi, umap-learn, tensorboard, pycocoevalcap, datasets, altair, gradio\n", + "Successfully installed SentencePiece-0.2.0 absl-py-2.1.0 accelerate-0.19.0 addict-2.4.0 aiofiles-23.2.1 aiohttp-3.9.4 aiosignal-1.3.1 altair-5.3.0 annotated-types-0.6.0 anyio-4.3.0 async-timeout-4.0.3 attrs-23.2.0 bitsandbytes-0.43.1 braceexpand-0.1.7 cachetools-5.3.3 click-8.1.7 contourpy-1.1.1 cycler-0.12.1 datasets-2.18.0 dill-0.3.8 einops-0.7.0 einops_exts-0.0.4 exceptiongroup-1.2.0 fastapi-0.110.1 ffmpy-0.3.2 filelock-3.13.4 fonttools-4.51.0 frozenlist-1.4.1 fsspec-2024.2.0 google-auth-2.29.0 google-auth-oauthlib-1.0.0 gradio-4.26.0 gradio-client-0.15.1 grpcio-1.62.1 h11-0.14.0 httpcore-1.0.5 httpx-0.27.0 huggingface-hub-0.22.2 importlib-metadata-7.1.0 importlib-resources-6.4.0 jinja2-3.1.3 joblib-1.4.0 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 kiwisolver-1.4.5 kornia-0.7.2 kornia-rs-0.1.3 llvmlite-0.41.1 markdown-3.6 markdown-it-py-3.0.0 markupsafe-2.1.5 matplotlib-3.7.5 mdurl-0.1.2 mmengine-0.10.3 multidict-6.0.5 multiprocess-0.70.16 nltk-3.8.1 numba-0.58.1 oauthlib-3.2.2 opencv-python-4.9.0.80 orjson-3.10.1 packaging-24.0 pandas-2.0.3 pkgutil-resolve-name-1.3.10 platformdirs-4.2.0 protobuf-5.26.1 psutil-5.9.8 pyarrow-15.0.2 pyarrow-hotfix-0.6 pyasn1-0.6.0 pyasn1-modules-0.4.0 pycocoevalcap-1.2 pycocotools-2.0.7 pydantic-2.7.0 pydantic-core-2.18.1 pydub-0.25.1 pygments-2.17.2 pynndescent-0.5.12 pyparsing-3.1.2 python-dateutil-2.9.0.post0 python-multipart-0.0.9 pytz-2024.1 referencing-0.34.0 regex-2023.12.25 requests-oauthlib-2.0.0 rich-13.7.1 rpds-py-0.18.0 rsa-4.9 ruff-0.3.7 safetensors-0.4.3 scikit-learn-1.3.2 scipy-1.10.1 semantic-version-2.10.0 shellingham-1.5.4 six-1.16.0 sniffio-1.3.1 starlette-0.37.2 tensorboard-2.14.0 tensorboard-data-server-0.7.2 threadpoolctl-3.4.0 tokenizers-0.15.2 tomli-2.0.1 tomlkit-0.12.0 toolz-0.12.1 transformers-4.39.3 typer-0.12.3 tzdata-2024.1 umap-learn-0.5.6 uvicorn-0.29.0 wcwidth-0.2.13 webdataset-0.2.86 websockets-11.0.3 werkzeug-3.0.2 xxhash-3.4.1 yapf-0.40.2 yarl-1.9.4 zipp-3.18.1\n", + "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n", + "\u001b[0m" + ] + }, + { + "output_type": "execute_result", + "data": { + "text/plain": [] + }, + "metadata": {}, + "execution_count": 11 + } + ] + }, + { + "cell_type": "code", + "source": [ + "%%shell\n", + "source activate brainx\n", + "pip install -r requirements.txt" + ], + "metadata": { + "id": "P6mS7pMY501e" + }, + "execution_count": null, + "outputs": [] + }, + { + "cell_type": "markdown", + "source": [ + "### Downloading Data and Checkpoints" + ], + "metadata": { + "id": "4kaukcZTmlce" + } + }, + { + "cell_type": "code", + "source": [ + "%%shell\n", + "destination=\"UMBRAE/umbrae/nsd_data\"\n", + "subdirs=(\"test\") # (\"train\" \"test\" \"val\")\n", + "for subdir in \"${subdirs[@]}\"; do\n", + " full_destination=\"${destination}/webdataset_avg_split/${subdir}/\"\n", + " mkdir -p \"$full_destination\"\n", + "done\n", + "\n", + "declare -a i_values=(1 2 5 7)\n", + "\n", + "# download the test set\n", + "for i in \"${i_values[@]}\"; do\n", + " for j in {0..1}; do\n", + " url=\"https://huggingface.co/datasets/pscotti/naturalscenesdataset/resolve/main/webdataset_avg_split/test/test_subj0${i}_${j}.tar\"\n", + " wget -P \"$full_destination\" \"$url\"\n", + " done\n", + "done" + ], + "metadata": { + "id": "KI3uiSSEmlDo" + }, + "execution_count": null, + "outputs": [] + }, + { + "cell_type": "code", + "source": [ + "%%shell\n", + "cd BrainHub\n", + "# download reference images\n", + "wget -P \"caption\" \"https://huggingface.co/datasets/weihaox/brainx/resolve/main/all_images.pt\"\n", + "python processing/decode_images.py" + ], + "metadata": { + "id": "-mFA5DGk3gyK" + }, + "execution_count": null, + "outputs": [] + }, + { + "cell_type": "code", + "source": [ + "%%capture\n", + "# download checkpoints\n", + "!python -c 'from huggingface_hub import snapshot_download; snapshot_download(repo_id=\"weihaox/brainx\", repo_type=\"dataset\", local_dir=\"UMBRAE/umbrae\", ignore_patterns=[\"all_images.pt\", \".gitattributes\"])'" + ], + "metadata": { + "id": "k0Kwf7k0x7gY" + }, + "execution_count": null, + "outputs": [] + }, + { + "cell_type": "markdown", + "source": [], + "metadata": { + "id": "pI_RocS3x5t0" + } + }, + { + "cell_type": "code", + "source": [ + "# !pip install torch\n", + "# !pip install torchvision\n", + "# !pip install braceexpand\n", + "# !pip install huggingface_hub\n", + "# !pip install webdataset\n", + "# !pip install transformers\n", + "# !pip install einops\n", + "# !pip install einops_exts\n", + "!pip install sentencepiece" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "AUG0gk_x435o", + "outputId": "517d39f0-e6aa-48e8-d42c-566420aed141" + }, + "execution_count": null, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "Collecting sentencepiece\n", + " Downloading sentencepiece-0.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.7 kB)\n", + "Downloading sentencepiece-0.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.3 MB)\n", + "\u001b[?25l \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m0.0/1.3 MB\u001b[0m \u001b[31m?\u001b[0m eta \u001b[36m-:--:--\u001b[0m\r\u001b[2K \u001b[91m━━━━━━━━━\u001b[0m\u001b[90m╺\u001b[0m\u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m0.3/1.3 MB\u001b[0m \u001b[31m9.1 MB/s\u001b[0m eta \u001b[36m0:00:01\u001b[0m\r\u001b[2K \u001b[91m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m\u001b[91m╸\u001b[0m \u001b[32m1.3/1.3 MB\u001b[0m \u001b[31m23.5 MB/s\u001b[0m eta \u001b[36m0:00:01\u001b[0m\r\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m1.3/1.3 MB\u001b[0m \u001b[31m16.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", + "\u001b[?25hInstalling collected packages: sentencepiece\n", + "Successfully installed sentencepiece-0.2.0\n", + "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n", + "\u001b[0m" + ] + } + ] + }, + { + "cell_type": "code", + "source": [ + "%%shell\n", + "prompt_caption='Describe this image as simply as possible.'\n", + "prompt_ground='Please interpret this image and give coordinates [x1,y1,x2,y2] for each object you mention.'\n", + "cd UMBRAE/umbrae\n", + "python inference.py --fmri_encoder 'brainx' --subj 1 --prompt \"$prompt_ground\" \\\n", + " --data_path 'nsd_data' --brainx_path 'train_logs/brainx.pth' \\\n", + " --save_path 'evaluation/eval_caption/caption_results/umbrae' --save_image True" + ], + "metadata": { + "id": "cDgKkMQUoqvT" + }, + "execution_count": null, + "outputs": [] + } + ] +} \ No newline at end of file diff --git a/umbrae/requirements.txt b/umbrae/requirements.txt index a8364ed..7c5587c 100644 --- a/umbrae/requirements.txt +++ b/umbrae/requirements.txt @@ -27,4 +27,5 @@ einops_exts kornia umap-learn pycocoevalcap -wcwidth \ No newline at end of file +wcwidth +huggingface_hub \ No newline at end of file