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Quickstart:

Requirements: docker, docker-compose

apt install -y docker-compose
git clone <this repo>
docker-compose up
# Install Docker
# https://docs.docker.com/install/linux/docker-ce/ubuntu/
sudo apt-get update

sudo apt-get install \
    apt-transport-https \
    ca-certificates \
    curl \
    software-properties-common

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -

sudo add-apt-repository \
   "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
   $(lsb_release -cs) \
   stable"

sudo apt update
sudo apt install -y docker-ce

# Install software in this repo
cd /opt
sudo git clone https://github.com/davehughes/radiograph
cd radiograph
sudo apt install -y virtualenv python2.7
sudo virtualenv env
sudo env/bin/pip install docker-compose
# Edit docker-compose.yml to add secrets/config as appropriate
# Download database backup to root directory, named 'radiograph-backup.sql'
sudo env/bin/docker-compose build
sudo env/bin/docker-compose up -d

File storage patterns:

  • original files stored as /[Genus] [species]/[institution][id][Genus][species][aspect].tif
  • Proposed: store files in corresponding directories:
    • /[original path]/[original basename]/original.tif
    •  ''         /        ''         /compressed.png
      
    •  ''         /        ''         /medium.png
      
    •  ''         /        ''         /thumb.png
      

Image processing:

  • Original images are ~7MB TIFFs at ~1800x1100 resolution
  • Derivatives, created using imagemagick's 'convert' utility:
    • Original size, PNG, compressed to ~850 KB/~12%
    • Medium, PNG, resized to fit within 800x800 resolution (~188KB)
    • Thumbnail, PNG, resized to fit within 120x120 resolution (~15KB)

About

Database of primate skull radiographs supporting Terry Ritzman's dissertation.

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