theowoo / plenoptic

Visualize/test models for visual representation by synthesizing images.

plenoptic

In recent years, adversarial examples have demonstrated how difficult it is to understand how complex models process images. The space of all possible images is impossibly vast and difficult to explore: even when training on millions of images, a dataset only represents a tiny fraction of all images.

plenoptic is a python library that provides tools to help researchers better understand their models by using optimization to synthesize novel informative images. These images allow us to build our intuition for what features the model ignores and what it is sensitive to. These synthetic images can then be used in psychophysics experiments for further investigation.

More specifically, all models have three components, inputs x, outputs y, and parameters θ. When working with models, we typically either simulate, by holding x and θ constant, and generating predictions for y, or fit, by holding x and y constant and using optimization to find the best-fitting θ. However, for optimization purposes, there's nothing special about x, so we can instead hold y and θ constant and use optimization to synthesize new inputs x. Synthesis methods do exactely that: they take a model with set parameters, set outputs and generate new inputs. They allow for better understanding of the model by assessing what it is sensitive to and, crucially, what it is not sensitive to, as well as generating novel stimuli for testing the model.

Here's a table summarizing this:

{x, y, θ} : inputs, outputs, parameters

	fixed	variable
simulate	{x, θ}	{y}
learn	{x, y}	{θ}
synthesize	{y, θ}	{x}

plenoptic contains the following four synthesis methods (with links to examples that make use of them):

• Metamers: given a model and a reference image, stochastically generate a new image whose model representation is identical to that of the reference image.
• Eigendistortions: given a model and a reference image, compute the image perturbation that produces the smallest and largest changes in the model response space. These correspond to the minimal/maximal eigenvectors of the Fisher Information matrix of the representation (for deterministic models, the minimal/maximal singular vectors of the Jacobian).
• Maximal differentiation (MAD) competition: given two models that measure distance between images and a reference image, generate pairs of images that optimally differentiate the models. Specifically, synthesize a pair of images that the first model says are equi-distant from the reference while the second model says they are maximally/minimally distant from the reference. Synthesize a second pair with the roles of the two models reversed.
• Geodesics: given a model and two images, synthesize a sequence of images that lie on the shortest ("geodesic") path in the model's representation space.

Status

This project is currently under heavy development. Not all features have been implemented, and there will be breaking changes.

Roadmap

See the github project for a more detailed roadmap, but at the high level:

• Short term:
  1. Finalize Portilla-Simoncelli texture model
  2. Recreate existing MADCompetition examples.
• Medium term:
  1. Finalize geodesics
  2. Get eigendistortion and geodesics to use Synthesis superclass
  3. Write more documentation and tutorials
  4. Finalize model API, create superclass
  5. Add more models
• Long term:
  1. Present at conference to advertise to users
  2. Submit paper to Journal of Open Source Software

NOTE

We currently support python 3.6, 3.7, and 3.8. See this issue for 3.9 status

Setup

These are instructions for how to install and run the development version of the plenoptic package (we are currently pre-release and not on pip, so this is the only way to use plenoptic).

The following instructions will work on Linux or Mac. If you're on Windows, I recommend looking into the Windows Subsystem for Linux.

System

If you have not setup python on your system before: install miniconda (this just contains python and conda, a very nifty package manager; choose python 3.7). Conda is separate from python: it's a package manager, which makes it easy to install a variety of python libraries. If you've ever used apt on Ubuntu or brew on Macs, then you've used a package manager before. Python has its own package manager, pip, which generally works very well, but in my experience I've found conda tends to work with fewer issues. See here for some more details, but the gist seems to be: conda can handle external (non-python) dependencies, whereas pip cannot, and conda can create virtual environments (see item 3 in this list), whereas pip cannot (the standard python way is to use virtualenv, which also works well). See here for a blog post from Jake VanderPlas with more details on conda.

You will probably need to restart your terminal for this to take effect. You should see base somewhere on your command line prompt.

Once you've done that, open the command-line and navigate to wherever you want to download this repository (for example, ~/Documents), and check that you have git installed on your system:

cd ~/Documents
which git

assuming the second command returns something (e.g., /usr/bin/git), git is installed and you're good to go. If nothing gets printed out, then you need to install git. See this cheatsheet for some more explanation of git, Github, and the associated terminology.

ffmpeg

Several methods in this package generate videos. There are several backends possible for saving the animations to file, see (matplotlib documentation)[https://matplotlib.org/stable/api/animation_api.html#writer-classes] for more details. In order convert them to HTML5 for viewing (and thus, to view in a jupyter notebook), you'll need ffmpeg installed and on your path as well.

To change the backend, run matplotlib.rcParams['animation.writer'] = writer before calling any of the animate functions. If you try to set that rcParam with a random string, matplotlib will tell you the available choices.

plenoptic

Once git is installed, you can clone the repository:

git clone https://github.com/LabForComputationalVision/plenoptic.git

Enter your username and password and, after a bit of a wait, you should have a brand new plenoptic folder, plenoptic. Let's navigate to that folder, create a new virtual environment, and install the package:

cd plenoptic
conda create -n plenoptic python==3.7
conda activate plenoptic
pip install -e .

We have now created a new virtual environment called plenoptic, which originally contains only the bare requirements (python, pip, etc.). We then activate it (which means that everything we do to interact with python will use this virtual environment, so only the python version and packages included there; you should see plenoptic somewhere on your command line prompt) and install plenoptic. This will install all the requirements necessary for plenoptic to run.

Jupyter

If you wish to locally run the notebooks, you will need to install jupyter and ipywidgets (you can also run them in the cloud using Binder). There are two main ways of getting a local jupyter install` working with this package:

1. Install jupyter in the same environment as plenoptic. If you followed the instructions above to create a conda environment named plenoptic, do the following:

conda activate plenoptic
conda install -c conda-forge jupyterlab ipywidgets

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.

2. Use nb_conda_kernels. Again, if you followed the instructions above:

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

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

In either case, to open the notebooks, navigate to the examples/ directory under this one on your terminal and activate the environment you install jupyter into (plenoptic for 1, base for 2), then run jupyter and open up the notebooks. If you followed the second method, you should be prompted to select your kernel the first time you open a notebook: select the one named "plenoptic".

Keeping up-to-date

Once you've downloaded and set up plenoptic for the first time, you can use git pull to keep it up-to-date. Navigate to the directory (if you downloaded plenoptic into your Documents folder above, that's cd ~/Documents/plenoptic) and run git pull origin main. git may yell at you if you've made local changes it can't figure out how to resolve. You'll have a merge conflict on your hands, see here for more information and how to proceed.

If you'd like to contribute any of the changes you've made, view the Contributing section.

Getting started

Once you've set everything up appropriately, navigate to the example directory, start up JupyterLab (which will open in a new browser tab), and start exploring the notebooks!

cd examples/
jupyter lab

The notebooks contain examples and tutorials, and have been numbered in a recommended order. They're all very much under development, and we would appreciate any feedback!

Contributing

For info on how to contribute, see the CONTRIBUTING file, including info on how to test the package and build its documentation.

Research notice

Please note that this repository is participating in a study into sustainability of open source projects. Data will be gathered about this repository for approximately the next 12 months, starting from June 2021.

Data collected will include number of contributors, number of PRs, time taken to close/merge these PRs, and issues closed.

For more information, please visit the informational page or download the participant information sheet.