foveated-metamers

This repo contains the code for a vision science experiment investigating how human perception changes across the visual field using behavioral experiments and computational models inspired by the earlys tages of visual processing. We use these models to investigate what people cannot see, an approach that has a long history of vision science. If we know what information people are insensitive to, we can discard it or randomize it, and the resulting image should appear unchanged from the original.

See the preprint or the VSS 2023 poster for scientific details. You may also be interested in the website we put together for browsing through the synthesized images, and the OSF for bulk downloading the images or the behavioral data. Finally, you may be interested in plenoptic, a software package for generating metamers (and more!) for your own models.

If you re-use some component of this project in an academic publication, see the citation section for how to credit us.

Usage

The data and code for this project are shared with the primary goal of enabling reproduction of the results presented in the associated paper. Novel analyses should be possible, but no guarantees.

To that end, we provide several entrypoints into the data for re-running the analysis, with a script to automate their download and proper arrangement.

As a note: snakemake commands create files. I recommend adding -n to any snakemake command when you run it for the first time. This will do a "dry run", so you can see what steps snakemake will take, without running anything.

The following steps will walk you through downloading the fully-processed data and recreating the figures, read further on in this README for details:

Clone this repo.
- Because we use git submodules, you'll also need to run the following two lines:
```
git submodule sync
git submodule update --init --recursive
```
Open config.yml and modify the DATA_DIR path to wherever you wish to download the data (see config.yml section for details on this file).
Install the required software:
- Install miniconda on your system for python 3.7.
- Install mamba: conda install mamba -n base -c conda-forge
- Navigate to this directory and run mamba env create -f environment.yml to install the environment.
- Run conda activate metamers to activate the python environment.
- Additionally, install inkscape, version equal to or greater 1.0.2. It seems like that, with inkscape version 1.2.2, all images are embedded at full resolution, leading to a massive increase in file size. I'm not sure what change causes this. It works as intended with inkscape 1.1
- Check if you have rsync available (you probably do) and install it if you don't (probably best to do so via a package manager).
Run python download_data.py synthesis_input mcmc_fits figure_input to download the data required to create the papers in the main figure (this is about 20GB).
Run snakemake -k -j N reports/paper_figures/fig-XX.svg (where N is the number of cores to use in parallel) to recreate a given figure from the paper (note the number must be 0-padded, i.e., fig-01.svg, not fig-1.svg). These will end up in the reports/paper_figures/ directory. Note that they are svgs, a vector file format. If your default image viewer cannot open them, your browser can. They can be converted to pdfs using inkscape or Adobe Illustrator.
If you wish to create all the figures from the main body of the text, run snakemake -k -j N main_paper_figures. If one job fails, this will continue to run the others (that's what the -k flag means).

If you wish to create the figures in the appendix as well:

Download the additional data required: python download_data.py stimuli freeman2011_check_output (this is about 14GB).
Run snakemake -k -j N reports/paper_figures/fig-AY-XX.svg (where XX must again be 0-padded, but Y does not) to create figure XX from appendix Y or snakemake -k -j N appendix_figures to create all the figures from appendices 1 through 5.
The figures in appendix 6 have been split off because they require an additional 24GB data set, so to create these:
- Download the additional data: python download_data.py mcmc_compare.
- Create a single figure with snakemake -k -j N reports/paper_figures/fig-A6-XX.svg or all of them with snakemake -k -j N appendix_figures_mcmc_compare.

Some notes about the above:

The workflow for figure creation looks intimidating: because parallelization is easy, I split up the process into many small jobs. Therefore, there's ~100 jobs for each of the above main_paper_figures and appendix_figures. Don't worry! They generally don't take that much time.
The complete workflow is very long (going back to preparing the images for metamer synthesis), and so sometimes snakemake can take a long time to determine what to run. This problem can get exacerbated if the file modification timestamps get thrown off, so that snakemake thinks it needs to re-create some of the existing files. To limit the search space and force snakemake to only consider figure-related rules, use the included reports/figure_rules.txt and the --allowed-rules flag: cat reports/figure_rules.txt | xargs snakemake -prk main_paper_figures --allowed-rules. You can pass any argument to snakemake, as long as the command ends with --allowed-rules.
Several of the figures in the paper (e.g., figure 4) include example metamers or other large images. We link these images into the figure, rather than embed them, until the very end, in order to reduce file size. Embedding them requires inkscape and an attached display (so it cannot be run on e.g., a compute cluster). You can do all the steps except embedding the large images by appending _no_embed to the file or target name. So, you would create reports/paper_figures/fig-04_no_embed.svg rather than reports/paper_figures/fig-04.svg to create that single figure, or call snakemake -k -j N main_paper_figures_no_embed / snakemake -k -j N appendix_figures_no_embed to create all of the main paper / appendix figures without embedding.
- This allows you to run everything except the embedding on one machine that may be more powerful but lack a display (such as a compute cluster), and then finish up on e.g., your laptop. However, the paths used to link images will almost certainly not work when moving to a different machine, so if you view fig-04_no_embed.svg, you will see empty red squares where the images should go. When embedding the images, we correct the paths, so this is not a problem.
- It is possible that snakemake will get confused when you switch machines and decide that it wants to re-run steps because the file modification timestamps appear out of order (this might happen, in particular, because of TEXTURE_DIR, which is used at the very beginning of the workflow; point it to something old or non-existant to avoid this!). To prevent this, use the same trick as above: append --allowed-rules embed_bitmaps_into_figures main_figures appendix_figures to any snakemake command to ensure that it will only run the embedding rule (and the main_figures / appendix_figures rules).

Reproducing someone else's research code is hard and, in all likelihood, you'll run into some problem. If that happens, please open an issue on this repo, with as much info about your machine and the steps you've taken as possible, and I'll try to help you fix the problem.

To understand what the snakemake command is doing, see the What's going on? section I wrote in the readme for another project (here's the zenodo doi in case that disappears).

What if I want to do more than recreate the figures?

I have focused on enabling others to recreate the figures, but you should be able to use this repo to do everything in the paper. In particular, you might want to:

... examine the metamers synthesized for this project

We've put together a website where you can browse all the metamers synthesized for this project, filtering and sorting by their metadata.

If you'd like to bulk download all of them, you can do so from the OSF page, see its README for how they're organized.

... synthesize some metamers

I don't recommend using this repo to do this unless you're trying to do exactly what I did (and even so, see here). If you want to synthesize your own metamers, see plenoptic for a better tested, better documented, and more general implementation of metamer synthesis (plus more!).

But if you still want to try to synthesize some metamers using the code in this repo, download the figure_input data set and look at the path of the downloaded metamers. You can use snakemake to create metamers like that, and most parts of the path are options related to metamer synthesis, see METAMER_TEMPLATE_PATH in config.yml, as well as the create_metamers rule in Snakefile to get a sense for what these are.

You can also use the foveated_metamers.utils.generate_metamer_paths function to generate the list of paths that I used for metamers in this experiment (it can also be called from the command-line: python -m foveated_metamers.utils). See the command-line's helpstring or the function's docstring for details, but here's an example: in order to get the path for one of the energy model metamers created with the llama target image for each scaling value used in the original vs. synth white noise comparison, run: python -m foveated_metamers.utils V1 --ref_image llama --seed_n 0. Note that this prints out the files on a single line, so you may want to redirect the output to a file for later viewing (append > mets.txt) or split it up for easier viewing (append | tr ' ' '\n').

To recreate any of my metamers, you'll also need to download the synthesis_input data set, which includes the target images we used, as well as statistics used for normalizing the models' representation.

You should also be aware that the pooling windows are very large once you get below scaling=0.1, so I would start with a larger window size. It is also strongly recommended to use a GPU, which will greatly speed up synthesis.

... see what the experiment was like

The OSF project contains a video of a single training run shown to participants before performing the energy model original vs. synthesized comparison task. In it, participants view the metamers for two target images (tiles and azulejos) at the smallest and largest scaling values for this comparison (.063 and .27), comparing them against the original image. Participants receive feedback in the training (the central dot turns green when they answer correctly) and are told their performance at the end of the run; no feedback was given in the actual experiment. It was expected that participants would get close to 100% on the easy trials (large scaling) and close to 50% on the hard trials (small scaling).

If you wish to try the experiment yourself, set up your environment for the experiment and download the experiment training tarball: python download_data.py experiment_training. You can then follow the instructions in the Training section of this readme (note that you won't be able to use the example_images.py script; if you're interested in this, open an issue and I'll rework it).

Note that the stimuli won't be rescaled by default: unless you have the exact same experimental set up as me (screen size 3840 by 2160 pixels, viewing distance of 40cm, 48.5 pixels per degree), you'll need to use the -p and -d flags when calling experiment.py to specify the size of your screen in pixels and degrees.

Also note that your monitor should be gamma-corrected to have a linear relationship between luminance and pixel value.

... run the full experiment

First, Set up your environment for the experiment and download the stimuli: python download_data.py stimuli.

You may also want to download the files used in the training and try that out.

For a given model and comparison, the full expeirment consists of 3 sessions, with 5 runs each. A single session lasts about an hour, with small breaks built in between runs, each of which lasts about 10 minutes. Each session contains 5 target images, so that each subject sees 15 of the total 20. All subjects see the first 10, then the final 10 are split into two groups, with even-numbered subjects seeing the first group, odd-numbered the second.

You'll need to generate presentation indices (which define what order the images are presented in; the ones for the training task are included in their tarball). To do so, use snakemake: snakemake -prk {DATA_DIR}/stimuli/{model_name}/task-split_comp-{comp}/{subj_name}/{subj_name}_task-split_comp-{comp}_idx_sess-{sess_num}_run-{run_num}.npy, where:

{DATA_DIR}: the DATA_DIR field from the config.yml file
{model_name}: either RGC_norm_gaussian (for the luminance model) or V1_norm_s6_gaussian (energy)
{comp}: one of met, ref, met-natural, ref-natural or ref-downsample-2. This should match the {comp} wildcard from the stimulus file you downloaded.
{subj_name}: has the form sub-##, where ## a 0-padded integer. If this integer lies between 0 and 7 (inclusive), this will be the same presentation order as used in our experiment.
{sess_num}: 0-padded itneger between 0 and 2 (inclusive). The session determines which set of 5 target images are included.
{run_num}: 0-padded integer between 0 and 4 (inclusive). Each run contains 3 target images, so that run-01 contains target images {A,B,C}, run-02 contains {B,C,D}, run-03 contains {C,D,E}, run-04 contains {D,E,A}, and run-05 contains {E,A,B}.

You'll probably want to generate all the indices for a subject for a given model and comparison at once. You can do that by generating the dummy file: snakemake -prk {DATA_DIR}/stimuli/{model_name}/task-split_comp-{comp}/{subj_name}/{subj_name}_task-split_comp-{comp}_idx_tmp.txt.

Then read the Run experiment section of this readme.

Note that the stimuli won't be rescaled by default: unless you have the exact same experimental set up as me (screen size 3840 by 2160 pixels, viewing distance of 40cm, 48.5 pixels per degree), you'll need to use the -p and -d flags when calling experiment.py to specify the size of your screen in pixels and degrees.

And note that the above options allow you to run the experiment on a setup that has a different screen size (both in pixels and in degrees) than the intended one, the metamers were created with this specific set up in mind. Things should be approximately correct on a different setup (in particular, double-check that images are cropped, not stretched, when presented on a smaller monitor), but there's no guarantee. If you run this experiment, with these stimuli, on a different setup, my guess is that the psychophysical curves will look different, but that their critical scaling values should approximately match; that is, there's no guarantee that all scaling values will give images that will be equally confusable on different setups, but the maximum scaling value that leads to 50% accuracy should be about the same. The more different the viewing conditions, the less likely that this will hold.

Also note that your monitor should be gamma-corrected to have a linear relationship between luminance and pixel value.

... refit the psychophysical curves

Follow the first three steps in the usage section, so that you have setup your environment and specified DATA_DIR. Then, download the behavioral data: python download_data.py behavioral_data.

From here, it's up to you. If you'd like to use your own procedure, the OSF readme describes the most relevant columns of the behavioral .csv files.

If you'd like to use my procedure (using MCMC to fit a hierarchical Bayesian model, fitting all images and subjects simultaneously but each metamer model and comparison separately), you can do so using snakemake: snakemake -prk {DATA_DIR}/mcmc/{model_name}/task-split_comp-{comp}/task-split_comp-{comp}_mcmc_{mcmc_model}_step-{step_size}_prob-{accept_prob}_depth-{tree_depth}_c-{num_chains}_d-{num_draws}_w-{num_warmup}_s-{seed}.nc, where:

{DATA_DIR}: the DATA_DIR field from the config.yml file
{model_name}: either RGC_norm_gaussian (for the luminance model) or V1_norm_s6_gaussian (energy)
{comp}: one of met, ref, met-natural, ref-natural or ref-downsample-2, depending on which comparison you wish to fit.
{mcmc_model}: which hierarchical model to fit to the data. partially-pooled is used in the main body of the paper, see the Methods section for details on it and appendix 6 for details on the other two. Only the met and ref comparisons have more than one subject, so the models are interchangeable for the rest.
- partially-pooled: fit image-level and subject-level effects, no interaction between them.
- unpooled: fit each psychophysical curve separately, no group effects.
- partially-pooled-interactions: fit image-level and subject-level effects, plus an interation term.
{seed}: computational seed for reproducibility, must be an integer.
the rest are all hyperparameters for MCMC, see numpyro documentation and examples for more details.

Note that I've had issues guaranteeing exact reproducibility, even with the same seed. I have not been able to track down why this is.

If you refit the curves using MCMC, you'll want to check the diagnostics, effective sample size (ESS) and $\hat{R}$. You can create a plot summarizing these for each variable with snakemake (just replace .nc with _diagnostics.png). Vethari et al., 2021 recommend that you look for $\hat{R} < 1.01$ for all variables.

You can download my fits to the data (python download_data.py mcmc_fits for the partially pooled model, python download_data.py mcmc_compare for the other two) or use foveated_metamers.utils.get_mcmc_hyperparams to see what hyper-parameters I used to fit each comparison.

Setup

The analyses were all run on Linux (Ubuntu, Fedora, and CentOS, several different releases). Everything should work on Macs. For Windows, I would suggest looking into the Windows Subsystem for Linux, as Windows is very different from the others.

Software requirements

The python environment discussed below are required regardless of what you wish to do. There are several additional requirements that are optional:

If you are using download_data.py, you'll need rsync, which you probably already have. If not, it's probably best to grab it via your OS's package manager.
If you are synthesizing metamers, you'll need ffmpeg. This is probably also already installed on your machine, but if not, a static build is probably the easiest way to go.
If you're using GPUs for image synthesis, you'll need the python package dotlockfile as well: pip install dotlockfile.
For embedding images into our figures (the last step of figure creation for about a third of the figures), you need inkscape, version equal to or greater than 1.0.2.
- We also need to know the location of your inkscape preference file. The default is probably correct, but see section config.yml for more details.
Appendix 3 contains a small comparison between the pooling windows used in this project and those found in Freeman and Simoncelli, 2011. If you wish to generate these windows yourself, you will need MATLAB along with Jeremy Freeman's metamer code and the matlabPyrTools toolbox. You may also download the windows from the OSF (python download_data freeman2011_check_output). See below for more details.

There's a separate python environment for running the environment, so install that if you're planning on running the experiment.

Python

This has been run and tested with version 3.7, unsure about more recent versions.

Install miniconda with the appropriate python version.
Install mamba: conda install mamba -n base -c conda-forge (I recommend using mamba instead of conda to install the environment because conda tends to hang while attempting to solve the environment).
After cloning this repo, run the following from this directory to grab the git submodules:
```
git submodule sync
git submodule update --init --recursive
```
In this directory, run mamba env create -f environment.yml
If everything works, type conda activate metamers to activate this environment.

As of fall 2022, the packages that I know have version requirements are specified in environment.yml. However, in case updates to the dependencies break something, I've included the output of the pip freeze command from two different machines (my laptop and Flatiron's compute cluster) at reports/pip_freeze_laptop.txt and reports/pip_freeze_hpc.txt, so a working environment is cached (note that this includes more packages than specified in environment.yml, because it includes all their dependencies as well).

I am also running tests on github actions to check that the following parts of the workflow run: the data download script, the included notebook, metamer synthesis, the pooling models, and fitting the MCMC curves. For all of these, I'm just testing that they can run, not the full workflow completes or that I get the proper outcome, but that should be sufficient to see what package versions are compatible. (I'm not testing figure creation, because I couldn't come up with a way to do that didn't require more storage than is available for free from Github runners --- if you have a solution for this, I'd love to hear it).

Jupyter

This repo includes one notebook, for examining the differences between this project and Freeman and Simoncelli, 2011. You can view the cached output of the notebook online, or you can install jupyter locally and run the notebook.

There are two main ways of installing jupyter locally:

Install jupyter in this metamers environment:

conda activate metamers
mamba install -c conda-forge jupyterlab

This is easy but, if you have multiple conda environments and want to use Jupyter notebooks in each of them, it will take up a lot of space.

Use nb_conda_kernels:

# activate your 'base' environment, the default one created by miniconda
conda activate 
# install jupyter lab and nb_conda_kernels in your base environment
mamba install -c conda-forge jupyterlab
mamba install nb_conda_kernels
# install ipykernel in the calibration environment
mamba install -n metamers ipykernel

This is a bit more complicated, but means you only have one installation of jupyter lab on your machine.

Experiment environment

Install miniconda and mamba as described above (you probably don't need the submodules, but they won't hurt), then run:

mamba env create -f environment-psychopy.yml

Then, to activate, run conda activate psypy.

PsychoPy provides multiple backends. I'm now using the pyglet backend, but I've occasionally had issues with a weird XF86VidModeGetGammaRamp failed error. That's just something to be aware of.

This environment-psychopy.yml file pins all the package versions but I didn't spend a lot of time trying to figure out what exactly was necessary or worry about the versions overly-much. That is to say, I think as long as you can get a working psychopy install with the pyglet backend, the code should work. So you could try just to install psychopy, pyglet, h5py (used for storing behavioral data) and numpy (stimuli are saved as numpy arrays) and go from there.

Data

Source images

We use images from the authors' personal collection and the UPenn Natural Image Database as the targets for our metamer generation. This is because we need images that are large, linear (i.e., their pixel intensities are proportional to photon count, as you get from an image that has not been processed in any way), and openly-licensed.

Authors' personal collection:
- WFB: azulejos, tiles, bike, graffiti, llama, terraces
- EPS: ivy, nyc, rocks, boats, gnarled, lettuce
UPenn Natural Image Database: treetop (cd01A/DSC_0033), grooming (cd02A/DSC_0011), palm (cd02A/DSC_0043), leaves (cd12A/DSC_0030), portrait (cd58A/DSC_0001), troop (cd58A/DSC_0008).
Unpublished photos from David Brainard: quad (EXPOSURE_ASC/DSC_0014), highway (SNAPSHOTS/DSC_0200).

.tiff files of all these images can be downloaded from the OSF page. They have been demosaiced (using DCRAW) but otherwise untouched from the raw files. For image synthesis they were converted to 16-bit grayscale png files, cropped / expanded to 2048 by 2600 pixels (Prof. Brainard's photos and those from the UPenn Natural Image Database were 2014 pixels tall and so a small amount of reflection padding was used on these photos), and rescaled so all pixel values lay between .05 and .95. These png files are found in the synthesis_input tarball on the OSF page.

Download data

The data for this project is available on its OSF page (almost everything) and NYU's Faculty Digital Archive (the files required for appendix 6, which are the fits using the alternative MCMC models). The OSF readme describes its contents in detail.

We also provide the download_data.py script, which downloads and arranges the data into the structure that snakemake expects. The following data sets can be downloaded with this script:

synthesis_input: the inputs required for synthesizing model metamers, this includes the original images whose model representation our metamers match and the set of statistics used to normalize model responses.
stimuli: numpy arrays containing the model metamers used as stimuli in our experiment for each model and comparison separately, along with csv files with their metadata.
behavioral_data: csv files containing participant responses, along with metadata (each model and comparison separate).
mcmc_fits: .nc files containing the fits of the partially pooled hierarchical model to behavior, for each model and comparison separately
figure_input: miscellaneous files not contained in the other data sets required to create the figures in the paper (some of the model metamers, etc.)
freeman2011_check_input, freeman2011_check_output: the input and output files for a brief comparison between our pooling windows and energy model metamers and those presented in Freeman and Simoncelli, 2011. See below for more details.
experiment_training: some files used to train participants, can also be viewed in order to get a sense for how the experiment was structured. See above for details.
mcmc_compare: .nc files containing the fits of the alternative MCMC models to behavior, as well as the csv files evaluating each MCMC models performance, used for appendix 6.

To download one of the above, call python download_data.py {TARGET_DATASET}, replacing {TARGET_DATASET} with one of the above. Make sure you have specified DATA_DIR in config.yml first. The script will give you an estimate of how large each data set is and ask if you would like to continue.

There are several components found on the OSF page that cannot be downloaded using download_data.py. These are made available because they might be useful for others, but I do not expect them to be used by anyone with this repo, because they are not necessary for reproducing the figures.

config.yml

This is configuration file containing options used by snakemake. You need to modify the first one, DATA_DIR, and might need to modify the other paths in that first section. All the other options should be left unmodified. The file is commented explaining what each of the options are.

Note that, unless stated otherwise, you cannot use ~ in any of the paths in this file (you must write out the full path to your home directory, e.g., /home/billbrod or /Users/billbrod). Also, the paths should probably not have capital letters -- there's a discrepancy between how Mac and Linux handle capital letters in paths, which might create problems.

Directory structure

Snakefile: used by snakemake to determine how to create the files for this project. Handles everything except the experiment.
foveated_metamers/: library of functions used in this project
- create_metamers.py: creates metamers.
- stimuli.py: assembles the various metamer images into format required for running the experiment.
- distances.py: finds distance in model space between images in an efficient way.
- experiment.py: runs experiment.
- analysis.py: basic analyses of behavioral data (gets raw behavioral data into format that can fit by psychophysical curves).
- curve_fit.py: fits psychophysical curves to real or simulated data using pytorch. We didn't end up using this method of fitting the curves.
- simulate.py: simulate behavioral data, for checking curve_fit.py performance, as well as how many trials are required.
- mcmc.py: use Markov Chain Monte Carlo (MCMC) to fit a probabilistic model of psychophysical curves with numpyro. This is how the curves presented in the paper were fit.
- statistics.py: compute some other image statistics (heterogeneity, Fourier amplitude spectra, etc).
- plotting.py: plotting functions.
- figures.py: creates various figures.
- compose_figures.py: combines plots (as created by functions in figures.py) into multi-panel figures.
- other_data.py: functions to fit a line (hinged or not) to the Dacey 1992 data, which gives the receptive field size of retinal ganglion cells. This also uses numpyro and so looks fairly similar to mcmc.py.
- create_mad_images.py: synthesize Maximally-Differentiating images (as in Wang and Simoncelli, 2008), to highlight mean-squared error remaining in human metamers.
- create_other_synth.py: other ways to synthesize images to highlight mean-squared error remaining in human metamers.
- observer_model.py: first steps towards an observer model to predict human performance when images are not metamers. Did not end up making much progress, so this is not present in the paper.
- utils.py: various utility functions.
- style.py: code for styling the figures.
extra_packages/: additional python code used by this repo. The bits that live here were originally part of plenoptic, but were pulled out because it's a bad idea for a research project to be so heavily reliant on a project currently under development.
- pooling-windows: git submodule that points to this repo, containing the pooling windows we use.
- plenoptic_part: contains the models and metamer synthesis code (as well as some utilities) that were pulled out of plenoptic, branching at this commit (I used git filter-repo and so the history should be preserved). While the model code (and some of the utilities) have been deleted from plenoptic and are unique to this repo, the synthesis code here is a modified version of the one in plenoptic. If you wish to use synthesis for your own work use the plenoptic version, which is regularly tested and supported.
notebooks/: jupyter notebooks for investigating this project in more detail.
- Freeman_Check.ipynb: notebook checking that our windows are the same size as those from Freeman and Simoncelli, 2011 (and thus that the models' scaling parameter has the same meaning); see below for more details.
examples_images.py: script to open up some example images to show participants before the experiment (see Training section for how to use).
download_data.py: script to download and arrange data for reproducing results and figures. See Download data for how to use.
matlab/: two matlab scripts using external matlab libraries. Neither are necessary: one is used to generate the windows from the Freeman and Simoncelli, 2011 paper (the output of which can be downloaded using download_data.py) and the other generates some LGN-like image statistics that we didn't end up using.
data/: contains some data files.
- Dacey1992_RGC.csv: csv containing data from figure 2B of Dacey and Petersen, 1992, extracted using WebPlotDigitizer on July 15, 2021. To recreate that figure, use the snakemake rule dacey_figure. Note that we did not separate the data into nasal field and temporal, upper, and lower fields, as the paper does.
- checksums.json: json file containing BLAKE2b hashes for the files downloadable via download_data.py, so we can check they downloaded corectly.
reports/: contains a variety of figure-related files.
- figures/: these are figure components that I use when putting the figures together. They fall into two categories: schematics that are copied as is, with no changes (e.g., image space schematics, experiment schematic), and templates that we embed images into (e.g., the example metamer figures).
- paper_figures/: these are the actual figures used in the paper, as created by the snakemake file. There are none in the github repo, see Usage section for details on how to create them.
- figure_rules.txt: this is a list of snakemake rules that create figures (rather than analyze the data). It can be used to limit snakemake's search of possible analysis paths. See Usage for details on how to use.
- pip_freeze_laptop.txt, pip_freeze_hpc.txt: the outputs of pip freeze on two different machines, showing working environments as of fall 2022.
tests/test_models.py: contains a small number of tests of the pooling models, ran weekly and on every push (alongside other tests).
environment-psychopy.yml, environment.yml: yml files defining conda environment for the experiment (using psychopy) and for everything. See Setup section for how to use.
greene.json, rusty.json: json files defining how snakemake should communicate with NYU's and Flatiron's SLURM clusters, respectively (works with the snakemake-slurm profile). I have written a section on how to use snakemake with a SLURM cluster in a readme for a different project, and may write something in more detail at some point. Reach out if you have questions.
config.yml: yml configuration file, defining paths, metamer path template, and some configuration for experiment structure, see here for details.

Usage details

The following sections contain some extra details that may be useful.

Check against Freeman and Simoncelli, 2011 windows

This project uses a modification of the pooling windows first described in Freeman and Simoncelli, 2011. We include some code to check our reimplementation of the windows and the extension to use Gaussians instead of raised-cosine falloffs. Basically, we want to make sure that our windows are the same size -- identical reimplementation is not important, but we want to make sure that the models' scaling parameter has the same interpretation; it should be the ratio between the eccentricity and the radial diameter of the windows at half-max amplitude. To do so, we include a notebook notebooks/Freeman_Check.ipynb, as well as some snakemake rules.

We check two things: that our windows' scaling parameter has the same meaning as that in the original paper, and that our V1 metamers look approximately the same. You can view this by looking at the Freeman_Check notebook and its cached outputs directly. If you wish to run the notebook locally, you'll need to download the input files (python download_data.py freeman2011_check_input) and then either download the files required (python download_data.py freeman2011_check_output) or generate them yourself (snakemake -prk freeman_check). Note that generating them yourself will require MATLAB with the Freeman metamer and matlabPyrTools toolboxes (set their paths correctly in config.yml)

Make sure you have Jupyter installed, then navigate to the notebooks/ directory on your terminal and activate the environment you install jupyter into (metamers or base, depending on how you installed it), then run jupyter and open up the notebook. If you used the nb_conda_kernels method, you should be prompted to select your kernel the first time you open a notebook: select the one named "metamers".

A portion of the results presented in this notebook are also found in one of the paper's appendices.

Experiment notes

These are the notes I wrote for myself so I remembered how to run the experiment and could teach others.

To run the experiment, make sure that the stimuli array and presentation indices have been generated and are at the appropriate path. It's recommended that you use a chin-rest or bite bar to guarantee that your subject remains fixated on the center of the image; the results of the experiment rely very heavily on the subject's and model's foveations being identical.

Training

To teach the subject about the experiment, we want to introduce them to the structure of the task and the images used. The first one probably only needs to be done the first time a given subject is collecting data for each model / comparison, the second should be done at the beginning of each session.

(The following paths all assume that DATA_DIR is ~/Desktop/metamers, replace that with your actual path.)

First, run a simple training run (if you haven't already, first run python download_data.py experiment_training to get the required files):
- conda activate psypy
- python foveated_metamers/experiment.py ~/Desktop/metamers/stimuli/training_noise/stimuli_comp-{comp}.npy sub-training 0 ; python foveated_metamers/experiment.py ~/Desktop/metamers/stimuli/training_{model}/stimuli_comp-{comp}.npy sub-training 0 where {comp} depends on which comparison you're running, and {model} is RGC_norm_gaussian or V1_norm_s6_gaussian, depending on which you're running.
- Explanatory text will appear on screen, answer any questions.
- This will run two separate training runs, both about one or two minutes, with feedback between each trial (the fixation dot will turn green if they answered correctly) and at the end of the run (overall performance).
- The first one will just be comparing natural to noise images and so the subject should get 100%. The goal of this one is to explain the basic structure of the experiment.
- The second will have two metamers, one easy and one hard, for each of two reference images. They should get 100% on the easy one, and about chance on the hard. The goal of this one is to show what the task is like with metamers and give them a feeling for what they may look like.
Run:
- conda activate metamers
- python example_images.py {model} {subj_name} {sess_num} where {model} is V1 or RGC depending on which model you're running, and {subj_name} and {sess_num} give the name of the subject and number of this session, respectively.
- This will open up three image viewers. Each has all 5 reference images the subject will see this session. One shows the reference images themselves, one the metamers with the lowest scaling value, and one the metamers with the highest scaling value (all linear, not gamma-corrected).
- Allow the participant to flip between these images at their leisure, so they understand what the images will look like.
- Note: this will not work unless you have the metamers for this comparison at the locations where they end up after synthesis (you probably don't). If you're interested in using this script, open an issue and I'll try to rework it.

Task structure

Unlike previous experiments, we use a split-screen task. Each trial lasts 1.4 seconds and is structured like so:

|Image 1 | Blank  |Image 2 |Response|  Blank |
|--------|--------|--------|--------|--------|
|200 msec|500 msec|200 msec|        |500 msec|

Image 1 will consist of a single image divided vertically at the center by a gray bar. One half of image 2 will be the same as image 1, and the other half will have changed. The two images involved are either two metamers with the same scaling value (if comp=met or met-natural) or a metamer and the reference image it is based on (if comp=ref or ref-natural). The subject's task is to say whether the left or the right half changed. They have as long as they need to respond and receive no feedback.

To run the experiment:

Activate the psypy environment: conda activate psypy
Start the experiment script from the command line:
- python foveated_metamers/experiment.py ~/Desktop/metamers/stimuli/{model}/stimuli_comp-{comp}.npy {subj_name} {sess_num} where {model}, {subj_name}, {sess_num}, {comp} are as described in the training section.
- There are several other arguments the experiment script can take, run python foveated_metamers/experiment.py -h to see them, and see the other arguments section for more information.
Explain the task to the subject, as given in the example below (similar text will also appear on screen before each run for the participant to read)
When the subject is ready, press the space bar to begin the task.
You can press the space bar at any point to pause it, but the pause won't happen until the end of the current trial, so don't press it a bunch of times because it doesn't seem to be working. However, try not to pause the experiment at all.
You can press q/esc to quit, but don't do this unless truly necessary.
There will be a break half-way through the block. The subject can get up, walk, and stretch during this period, but remind them to take no more than a minute. When they're ready to begin again, press the space bar to resume.
The data will be saved on every trial, so if you do need to quit out, all is not lost. If you restart from the same run, we'll pick up where we left off.
The above command will loop through all five runs for a given session. To do a particular set of runs pass -r {run_1} {run_2} ... {run_n} to the call to experiment.py (where {run_1} through {run_n} are 0-indexed integers specifying the runs to include). For example, if you quit out on the third run and wanted to finish that one and then do runs 4 and 5, pass: -r 2 3 4. If you just want to finish that run, you'd only pass -r 2.

Recommended explanation to subjects:

In this experiment, you'll be asked to complete what we call an "2-Alternative Forced Choice task": you'll view an image, split in half, and then, after a brief delay, a second image, also split in half. One half of the second image will be the same as the first, but the other half will have changed. Your task is to press the left or right button to say which half you think changed. All the images will be presented for a very brief period of time, so pay attention. Sometimes, the two images will be very similar; sometimes, they'll be very different. For the very similar images, we expect the task to be hard. Just do your best!

You'll be comparing natural and synthesized images. The first image can be either natural or synthesized, so pay attention! You will receive no feedback, either during or after the run.

For this experiment, fixate on the center of the image the whole time and try not to move your eyes.

The run will last for about twelve minutes, but there will be a break halfway through. During the break, you can move away from the device, walk around, and stretch, but please don't take more than a minute.

This part will not be shown on screen, and so is important:

You'll complete 5 runs total. After each run, there will be a brief pause, and then the instruction text will appear again, to start the next run. You can take a break at this point, and press the spacebar when you're ready to begin the next run.

Other arguments

The experiment.py takes several optional arguments, several of which are probably relevant in order to re-run this on a different experiment set up:

--screen / -s: one integer which indicate which screens to use.
--screen_size_pix / -p: two integers which indicate the size of the screen(s) in pixels .
--screen_size_deg / -d: a single float which gives the length of the longest screen side in degrees.

For more details on the other arguments, run python foveated_metamers/experiment.py -h to see the full docstring.

NOTE: While the above options allow you to run the experiment on a setup that has a different screen size (both in pixels and in degrees) than the intended one, the metamers were created with this specific set up in mind. Things should be approximately correct on a different setup (in particular, double-check that images are cropped, not stretched, when presented on a smaller monitor), but there's no guarantee. If you run this experiment, with these stimuli, on a different setup, my guess is that the psychophysical curves will look different, but that their critical scaling values should approximately match; that is, there's no guarantee that all scaling values will give images that will be equally confusable on different setups, but the maximum scaling value that leads to 50% accuracy should be about the same. The more different the viewing conditions, the less likely that this will hold.

Experiment Checklist

The following is a checklist for how to run the experiment. Print it out and keep it by the computer.

Every time:

Make sure monitor is using the correct icc profile (linear-profile; everything should look weirdly washed out). If not, hit the super key (the Windows key on a Windows keyboard) and type icc, open up the color manager and enable the linear profile.

First session only (on later sessions, ask if they need a refresher):

Show the participant the set up and show the participants the wipes and say they can use them to wipe down the chinrest and button box.
Tell the participant:

In this task, a natural image will briefly flash on screen, followed by a gray screen, followed by another image. Half of that second image will be the same as the first, half will have changed. Your task is to say which half has changed, using these buttons to say "left" or "right". You have as long as you'd like to respond, and you will not receive feedback. There will be a pause halfway through, as well as between runs; take a break and press the center button (labeled "space") to continue when you're ready. You won't press the buttons in the bottom row.

Train the participant. Say:

Now, we'll do two brief training runs, each of which will last about a minute. In the first, you'll be comparing natural images and noise; the goal is so you understand the basic structure of the experiment. In the second, you'll be comparing those same natural images to some of the stimuli from the experiment; some will be easy, some hard. You'll receive feedback at the end of the run, to make sure you understand the task. I'll remain in the room to answer any questions.

There will be fixation dot in the center of some explanatory text at the beginning, use that to center yourself.

Run (replace {model} with V1_norm_s6_gaussian or RGC_norm_gaussian):

conda activate psypy
python foveated_metamers/experiment.py ~/Desktop/metamers/stimuli/training_noise/stimuli_comp-ref.npy sub-training 0 ; python foveated_metamers/experiment.py ~/Desktop/metamers/stimuli/training_{model}/stimuli_comp-ref.npy sub-training 0

Answer any questions.

Every time:

Show the participant the images they'll see this session, replacing {model} with V1 or RGC (no need to use the full name), and {subj_name} and {sess_num} as appropriate:

conda activate metamers
python example_images.py {model} {subj_name} {sess_num}

Say the following and answer any questions:

These are the natural images you'll be seeing this session, as well as some easy and hard stimuli. You can look through them for as long as you'd like.

Ask if they have any questions before the experiment.
Say:

This will run through all 5 runs for this session. Each should take you 10 to 12 minutes. Come get me when you're done. As a reminder, you have as long as you'd like to respond, and you won't receive any feedback.

Run, replacing {model}, {subj_name}, {sess_num} as above:

conda activate psypy
python foveated_metamers/experiment.py ~/Desktop/metamers/stimuli/{model}/stimuli_comp-ref.npy {subj_name} {sess_num}

Known issues

When using multiprocessing (as done when fitting the psychophysical curves) from the command-line, I get OMP: Error #13: Assertion faliure at z_Linux_util.cpp(2361) on my Ubuntu 18.04 laptop. As reported here, this is a known issue, and the solution appears to be to set an environmental variable: running export KMP_INIT_AT_FORK=FALSE in the open terminal will fix the problem. Strangely, this doesn't appear to be a problem in a Jupyter notebook, but it does from IPython or the snakemake calls. I tried to set the environmental variable from within Snakefile, but I can't make that work. Running the calls with use_multiproc=False will also work, though it will obviously be much slower.
When trying to use the embed_bitmaps_into_figure rule on a drive mounted using rclone (I had my data stored on a Google Drive that I was using rclone to mount on my laptop), I got a 'Bad file descriptor' error from python when it tried to write the snakemake log at the end of the step. It appears to be this issue, adding the --vfs-cache-mode writes flag to the rclone mount command worked (though I also had to give myself full permissions on the rclone cache folder: sudo chmod -R 777 ~/.cache/rclone).
As of June 2023, there appears to be some issue with svgutils and inkscape, where any svg file that is the output of my compose_figures rule cannot be opened by inkscape (attempting to do so leads inkscape to immediately crash). This means that none of the files in the compose_figures directory can be used as inputs to the embed_bitmaps_into_figures rule (but those infigures can be). I'm unclear why this is happening now, but have been unable to track it down.

Notes on reproducibility

The intention of sharing this code is to allow for the reproduction of the figures in the resulting paper. This is the code I used to synthesize the metamers used in the experiment, and you can use it to do so, but there are a couple things you should be aware of:

Results will not be identical on CPUs and GPUs. See PyTorch's notes on this.
I used stochastic weight averaging (SWA) for the energy model metamers. SWA seems to reduce the final loss by averaging metamer pixel values as we get near convergence (see here for more details). However, the version of SWA I used to generated the metamers for the experiment was from torchcontrib, which was archived in 2020 and is no longer maintained (github repo). In May 2022, I noticed that the torchcontrib SWA implementation no longer worked on my tests with the most recent versions of python (3.10) and pytorch (1.12), so I updated my code to work with the pytorch SWA implementation. The resulting metamers are not identical to the ones produced before, but they are similar in both visual quality and loss, and I believe they would be indistinguishable in a 2AFC task.
The metamer synthesis code found here (in extra_packages/plenoptic_part) was very much a work in progress throughout this whole project and ended up becoming a tangled rats nest, as is the case for most research code.

For all the above reasons, I am sharing the synthesized metamers used in this experiment and recommend you use them directly if you need the exact images I used (to replicate my behavioral results, for example). If you wish to synthesize new metamers, whether using your own model or even using the ones from this paper, I strongly recommend you use the metamer synthesis code found in plenoptic, which is actively maintained and tested, though it is not identical to the procedure used here. Most important, it does not include a SWA implementation and probably will never include one, but I would be happy to help come up with how to add it in an extension or a fork.

Related repos

If you would like to generate your own metamers, see plenoptic, a python library for image synthesis, including metamers, MAD Competition, eigendistortions, and geodesics.

If you would like to use the pooling windows, see pooling-windows. This includes pytorch implementations of the Gaussian windows from this project, as well as the raised-cosine windows from Freeman and Simoncelli, 2011. The README describes how to use them for creating a version of the pooled luminance and energy models used in this project. Feel free to use the models in this repo, but the simpler version from that README may better suit your needs. The version in this repo includes a bunch of helper code, including for creating plots and the starts of paths not taken. The only important thing missing from the pooling-windows repo is normalization -- look for the normalize_dict attribute in extra_packages/plenoptic_part/simulate/ventral_stream.py to see how I implemented that, and feel free to reach out if you have trouble.

You may also be interested in the code used by two other papers that this project references a lot, Freeman and Simoncelli, 2011 and Wallis et al., 2019. If you wish to use the Freeman code, note the bug in window creation pointed out by Wallis et al. (discussed in their appendix 1).

Citation

If you use the data, code, or stimuli from this project in an academic publication, please cite the preprint. If you use the code, please additionally cite the zenodo doi for the corresponding release (e.g., v1.0-biorxiv corresponds to the DOI https://doi.org/10.5281/zenodo.7948552).

References

Dacey, D. M., & Petersen, M. R. (1992). Dendritic field size and morphology of midget and parasol ganglion cells of the human retina. Proceedings of the National Academy of Sciences, 89(20), 9666–9670. http://dx.doi.org/10.1073/pnas.89.20.9666
Freeman, J., & Simoncelli, E. P. (2011). Metamers of the ventral stream. Nature Neuroscience, 14(9), 1195–1201. http://dx.doi.org/10.1038/nn.2889
Vehtari, A., Gelman, A., Simpson, D., Carpenter, B., & Paul-Christian B"urkner (2021). Rank-normalization, folding, and localization: an improved $R$ for assessing convergence of mcmc (with discussion). Bayesian Analysis, 16(2), 667–718. http://dx.doi.org/10.1214/20-BA1221
Wallis, T. S., Funke, C. M., Ecker, A. S., Gatys, L. A., Wichmann, F. A., & Bethge, M. (2019). Image content is more important than bouma's law for scene metamers. eLife, 8(), . http://dx.doi.org/10.7554/elife.42512
Wang, Z., & Simoncelli, E. P. (2008). Maximum differentiation (MAD) competition: A methodology for comparing computational models of perceptual discriminability. Journal of Vision, 8(12), 1–13. http://dx.doi.org/10.1167/8.12.8

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foveated-metamers

Table of Contents

Usage

What if I want to do more than recreate the figures?

... examine the metamers synthesized for this project

... synthesize some metamers

... see what the experiment was like

... run the full experiment

... refit the psychophysical curves

Setup

Software requirements

Python

Jupyter

Experiment environment

Data

Source images

Download data

config.yml

Directory structure

Usage details

Check against Freeman and Simoncelli, 2011 windows

Experiment notes

Training

Task structure

Other arguments

Experiment Checklist

Known issues

Notes on reproducibility

Related repos

Citation

References

About

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Name		Name	Last commit message	Last commit date
Latest commit History 1,675 Commits
.github/workflows		.github/workflows
data		data
extra_packages		extra_packages
foveated_metamers		foveated_metamers
matlab		matlab
notebooks		notebooks
reports		reports
tests		tests
.gitignore		.gitignore
.gitmodules		.gitmodules
LICENSE		LICENSE
README.md		README.md
Snakefile		Snakefile
config.yml		config.yml
download_data.py		download_data.py
environment-psychopy.yml		environment-psychopy.yml
environment.yml		environment.yml
example_images.py		example_images.py
greene.json		greene.json
rusty.json		rusty.json

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foveated-metamers

Table of Contents

Usage

What if I want to do more than recreate the figures?

... examine the metamers synthesized for this project

... synthesize some metamers

... see what the experiment was like

... run the full experiment

... refit the psychophysical curves

Setup

Software requirements

Python

Jupyter

Experiment environment

Data

Source images

Download data

config.yml

Directory structure

Usage details

Check against Freeman and Simoncelli, 2011 windows

Experiment notes

Training

Task structure

Other arguments

Experiment Checklist

Known issues

Notes on reproducibility

Related repos

Citation

References

About

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Releases 1

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Contributors 6

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