Medical Image Tagger

The project is designed for Harvard Medical School. Users can put some tags for an medical image within the system.

Installation Guide

NOTE:

• We're going to assume that you have installed Python 2.7 and MySQL 5.x on your computer.

Install Django

NOTE: Python 2.7 required

1. Install pip

   For Unbuntu/Mint Users:

   apt-get install python-pip

   Or you can get standalone pip installer.

2. Install Django using pip

   For users who has installed pip

   pip install django==1.7.6

   Or you can install Django manually.

   Tip: Know more information on install Django at https://docs.djangoproject.com/en/1.6/intro/install/

Set up MITagger

1. Open mitagger/settings.py.
2. Edit your database configuration at line 59.

Set up Database

1. To connect MySQL in Python, we need install mysql-python first. You can install it using pip:

   pip install mysql-python

   Tip: If you get error message like this: EnvironmentError: mysql_config not found.

   Reference: http://stackoverflow.com/questions/7475223/mysql-config-not-found-when-installing-mysqldb-python-interface

2. Create database named mitagger in MySQL.

3. Use following command to create tables in the database:

   cd /path/to/the/app
   python manage.py syncdb

Install Additional Package

1. Install libtiff to Convert tiff to jpg

   For Ubuntu/Mint Users:

   apt-get install libtiff5 libtiff5-dev
   pip install --upgrade setuptools
   pip install --upgrade pip
   pip install numpy
   pip install -e svn+http://pylibtiff.googlecode.com/svn/trunk/

2. Install Wand to Convert tiff to jpg

   For Ubuntu/Mint Users:

   apt-get install libmagickwand-dev
   pip install Wand

3. Install NLTK to process natural language

   For Ubuntu/Mint Users:

   apt-get install libyaml-dev
   pip install nltk

4. Download NLTK Data

   python 
   >>> import nltk 
   >>> nltk.download() 
   # Press d to start downloading 
   >>> d 
   # Type all to download all packages 
   >>> all 

5. Install Elasticsearch

   For Ubuntu/Mint Users: Elasticsearch is running on Java, if you don't have a JRE on your machine, please install one.

   For example, We use OpenJDK7:

   apt-get install openjdk-7-jre

   Download and install the Public Signing Key

   wget -qO - http://packages.elasticsearch.org/GPG-KEY-elasticsearch | sudo apt-key add -

   Add the following to your /etc/apt/sources.list to enable the repository

   deb http://packages.elasticsearch.org/elasticsearch/1.3/debian stable main

   Run apt-get update and the repository is ready for use. You can install it with :

   apt-get install elasticsearch

   For RHEL/CentOS Users: Download and install the Public Signing Key

   rpm --import http://packages.elasticsearch.org/GPG-KEY-elasticsearch

   Add the following in your /etc/yum.repos.d/ directory in a file named (for example) elasticsearch.repo

   [elasticsearch-1.3]
   name=Elasticsearch repository for 1.3.x packages
   baseurl=http://packages.elasticsearch.org/elasticsearch/1.3/centos
   gpgcheck=1
   gpgkey=http://packages.elasticsearch.org/GPG-KEY-elasticsearch
   enabled=1

   And your repository is ready for use. You can install it with :

   yum install elasticsearch

   Install Elasticsearch bind for python:

   pip install elasticsearch

Start Server

1. If you want to use this application on a production site, use Apache with mod_wsgi.

   Tip: Get more information at https://docs.djangoproject.com/en/1.6/howto/deployment/wsgi/modwsgi/

2. If you just want to experiment with this application, just use following command:

   python manage.py runserver

   If you will get following output,

   May 14, 2014 - 04:50:57
   Django version 1.6.4, using settings 'mitagger.settings'
   Starting development server at http://127.0.0.1:8000/
   Quit the server with CONTROL-C.

   The application is deployed successfully. And you can use the application by visit http://127.0.0.1:8000 in web browser.