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Self-Supervised RGBD Reconstruction From Brain Activity 🧠

Official PyTorch implementation & pretrained models for:

More Than Meets the Eye: Self-Supervised Depth Reconstruction From Brain Activity
Guy Gaziv, Michal Irani

Self-Supervised Natural Image Reconstruction and Large-Scale Semantic Classification From Brain Activity
Guy Gaziv*, Roman Beliy*, Niv Granot*, Assaf Hoogi, Francesca Strappini, Tal Golan, Michal Irani

Summary

Setup

Code & environment

Clone this repo and create a designated conda environment using the env.yml file:

cd SelfSuperReconst
conda env create --name <envname> --file=env.yml
conda activate <envname>
pip install -e .

Data

This code requires all necessary data to be placed/linked under data folder in the structure below.
For completeness and ease of demo, we release the data for download HERE.
The following convenience script sets up all data automatically.

cd SelfSuperReconst
./setup_data.sh

/data
┣ 📂 imagenet
┃	┣ 📂 val
┃ 	┃	┗ (ImageNet validation images by original class folders)

┣ 📂 imagenet_depth
┃	┣ 📂 val_depth_on_orig_small_png_uint8
┃	┃	┗ (depth component of ImageNet validation images using MiDaS small model)
┃	┣ 📂 val_depth_on_orig_large_png_uint8
┃	┃	┗ (depth component of ImageNet validation images using MiDaS large model)

┣ 📂 imagenet_rgbd
┃	┗	(pretrained depth-only & RGBD vgg16/19 model checkpoints optimized for ImageNet classification challenge; These are used as Encoder backbone net or as a reconstruction metric)

┣ 📜 images_112.npz (fMRI on ImageNet stimuli at resolution 112x112)
┣ 📜 rgbd_112_from_224_large_png_uint8.npz (saved RGBD data at resolution 112, depth computed on 224 stimuli using MiDaS large model and saved as PNG uint8)
┣ 📜 sbj_<X>.npz (fMRI data)
┗ 📜 model-<X>.pt (MiDaS depth estimation models)

Training

The scripts folder provides most of the basic utility and experiments. In a nutshell, the training is comprised of two phases: (i) Encoder training implemented in train_encoder.py, followed by (ii) Decoder training, implemented in train_decoder.py. Each of those scripts need be run with the relevant flags which are listed in config files. General flags for both Encoder & Decoder training are listed in config.py, and Encoder/Decoder-training specific flags in config_enc.py or config_dec.py, respectively. Make sure to set the tensorboard_log_dir and gpu variables within the scripts. Note that decoder training assumes existence of a (pretrained) encoder checkpoint. We further provide general functionality tests to be used with pytest.

Example 1 (RGB-only):

Train RGB-only Encoder (supervised-only):

python $(scripts/train_enc_rgb.sh)

Then train RGB-only Decoder (supervised + self-supervised):

python $(scripts/train_dec_rgb.sh)

The results (reconstructions of train and test images) will appear under results. Detailed tensorboard logs will output under <tensorboard_log_dir> (to be set within the scripts).

Example 2 (Depth-only):

python $(scripts/train_enc_depth.sh) followed by python $(scripts/train_dec_depth.sh)

Example 3 (RGBD):

python $(scripts/train_enc_rgbd.sh) followed by python $(scripts/train_dec_rgbd.sh)

Tensorboard Logs

Evaluation

The eval.ipynb notebook provides functionality for evaluating reconstruction quality via n-way identification experiments (two types: % correct or rank identification, see paper). The DataFrame with evaluation results is saved under eval_results folder as a .pkl file. The eval_plot.ipynb loads these data and implements some basic visualization and printing of results.

Acknowledgments

Citation

If you find this repository useful, please consider giving a star ⭐️ and citation:

@article{Gaziv2021MoreActivity,
	title = {{More Than Meets the Eye: Self-Supervised Depth Reconstruction From Brain Activity}},
	author = {Gaziv, Guy and Irani, Michal},
	journal={arXiv preprint arXiv:2106.05113},
	year = {2021}
}

@article{Gaziv2022,
	title = {{Self-Supervised Natural Image Reconstruction and Large-Scale Semantic Classification from Brain Activity}},
	author = {Gaziv, Guy and Beliy, Roman and Granot, Niv and Hoogi, Assaf and Strappini, Francesca and Golan, Tal and Irani, Michal},
	journal = {NeuroImage},
	doi = {10.1016/J.NEUROIMAGE.2022.119121},
	year = {2022}
}