espiownage 0.0.27

Ownage of ESPI image inference

espiownage

Ownage (domination) of ESPI image inference. (Pronounced like "espionage" but with a little "own" in the middle.)

Welcome to the new phase of SPNet developement -- IN PROGRESS.
In this incarnation, we'll be making it an image-segmentation code instead of an object detector, and we'll use fast.ai.

Install

Preliminaries

Ubuntu (& probably other Linuxes):

sudo apt-get install python3-tk

Mac (with Homebrew)

brew install python-tk

Then on all systems, let's set up a virtual environment called espi. I like to put my environments in ~/envs:

mkdir ~/envs; python3 -m venv ~/envs/espi; source ~/envs/espi/bin/activate

And then you want/need to update pip in case it gave you an ancient version:

python3 -m pip install pip --upgrade

Then to install this package all you do is...

pip install espiownage

Note: the requirements on this package follow a "kitchen sink" approach so that everything a student might need gets installed, e.g. jupyter and more. (And wheel because it speeds up the installations...I think.)

How to use

If you're reading this, you probably have access to the "real" data, which sits (on my machine) in ~/Dropbox/Data/espiownage-data. So cd to that directory, i.e.,

$ cd ~/Dropbox/Data/espiownage-data

...(or whereever you've got it) for what follows.

AND THEN, so we don't "clobber" each other's work, make your own copy (~17MB) of the main annotations directory, as in append your last name (hawley, morrison, morgan, etc):

cp -r annotations annotations_yourlastname

and then we'll each edit our own copy just to avoid...confusion.

Note:If you don't have access to the real data, you can still grab the fake SPNet data and then, for each of those datasets: Move (or symlink) all the images to a directory called images/, and all the .csv files to a directory called annotations/, and proceed.

ellipse editor

ellipse_editor --files=annotations_yourlastname/*.csv

See ellipse_editor -h for command-line options. You can, for example, edit only one strike's worth of data by running

ellipse_editor --files=annotations_yourlastname/06241902*.csv

or a range of annotations, as in ellipse editor --files=annotations_yourlastname/06241902_proc_001*.csv

generate segmentation masks

...from annotations:

gen_masks --files=annotations/*.csv

Contributing / Development

You'll want to install more things:

pip install nbdev twine 

Fork this repo. When you want to update your repo, one macro does it all (see Makefile):

make git_update

Asides

Handy tips for students

I can never remember how to start up virtual environments / or I don't want to remember. So in my ~/.bashrc file (you may have a ~/.zshrc) I put in a line where I define an alias/function I call gimme, that reads like so:

gimme() { source ~/envs/"$1"/bin/activate;  }

(note that in order for this alias to be recognized, you need to either logout and log back in or else run $ source ~/.bashrc)

Then when I want to load environment like espi I just type...

gimme espi

--Scott H. Hawley, September 2021