RIMS (Region of Interest Management System)

A framework for maganing and visualization images and/or Regions Of Interest (ROI) recorded by an imaging system with frontend tools to visualize mosaics of images filtered by size, datetime, and morphological features.

Requirements

• python
• django
• postgresql
• gunicorn
• nginx

Installation

Preliminaries

Clone the RIMS repo and cd into it. From there follow the Digital Ocean setup instructions for Django with Postgres, Nginx, and Gunicorn on Ubuntu 20.04.

Install Python Packages

Install the following extra Django management functionality via pip

$ pip install django-extensions django-mptt django-jquery django-rest-framework django-cors-headers

Make sure to incude the apps in the rims/settings.py:

INSTALLED_APPS = [
    'django.contrib.admin',
    'django.contrib.auth',
    'django.contrib.contenttypes',
    'django.contrib.sessions',
    'django.contrib.messages',
    'django.contrib.staticfiles',
    'jquery',
    'django_extensions',
    'rest_framework',
    'corsheaders',
    'mptt',
    'rois',
]

Then install a few further packages for the image processing routines and pretty error logging.

$ pip install opencv-python scikit-image loguru

Update service to reload

Tell gunicorn to automatically reload upon edit by changing ExecStart in etc/systemd/gunicorn.service

ExecStart=/home/rimsadmin/software/rims/rimsenv/bin/gunicorn \
	--access-logfile - \
	--workers 4 \
	--reload \
	--bind unix:/run/gunicorn.sock \
	rims.wsgi:application

Tests

Run unit tests with Django's [https://docs.djangoproject.com/en/4.0/topics/testing/overview/](test features). In the ROIs directory write test models that will function in that framework:

from django.test import TestCase
from scripts.import_images_from_dir import do_import, run

# Create your tests here.
class ImportTestCase(TestCase):
    run('rois/test_images', 'rois/default_proc_settings.json')

Put a small set of images into the rois/test_images file and make sure the json settings file exists in the correct place. There are four images included in static/examples/test_images that can be used for this purpose. Currently these images will be removed each time you run the test import.

From the command line while in the database virtual environment run:

$ python manage.py test rois.tests

This command should spin up a small test database and run the import_images_form_dir.py script

Import images from directory

$ ./manage.py runscript import_images_from_dir --script-args /path/to/temp/image_directory /path/to/processing/settings.json

Where /path/to/temp/image_directory is a directory of raw images to import, and /path/to/processing/settings.json is the path to the proc_settings JSON file, typically in rois/default_proc_settings.json

Access web browser

Access the user interface by going to http://deeprip.shore.mbari.org/static/spcview/spcview.html#

You should see a mosaic like the one below