Install OpenREM 0.8.0b2¶
pip install openrem==0.8.0b4
Will need ``sudo`` or equivalent if installing on linux without using a virtualenv
Install pynetdicom (edited version)¶
Pynetdicom is used for the DICOM Store SCP and Query Retrieve SCU functions. See DICOM Store and QR for details.
pip install https://bitbucket.org/edmcdonagh/pynetdicom/get/default.tar.gz#egg=pynetdicom-0.8.2b2
Locate install location¶
- Ubuntu linux:
- Other linux:
- Linux virtualenv:
- Windows virtualenv:
There are two files that need renaming:
Windows notepad will not recognise the Unix style line endings. Please use an editor such as Notepad++ or Notepad2 if you can, else use WordPad – on the View tab you may wish to set the Word wrap to ‘No wrap’
In local_settings.py, always use forward slashes and not backslashes, even for paths on Windows systems.
The directories in this local_settings.py file must already exist - OpenREM will not create them for you.
SQLite is great for getting things running quickly and testing if the setup works, but is not recommended for production use.
We recommend using PostgreSQL as it is the best supported database for Django, and the only one for which the median value will be calculated and displayed in OpenREM charts. Alternatively, other databases such as MySQL/MariaDB, Oracle, and some others with lower levels of support can be used.
There are some further guides to setting up PostgreSQL – see Databases
If you are using SQLite:
'ENGINE': 'django.db.backends.sqlite3', 'NAME': '/ENTER/PATH/WHERE/DB/FILE/CAN/GO',
- Linux example:
- Windows example:
If you are using PostgreSQL:
'ENGINE': 'django.db.backends.postgresql_psycopg2', 'NAME': 'openremdb', 'USER': 'openremuser', 'PASSWORD': 'openrem_pw',
Location for imports and exports¶
Csv and xlsx study information exports and patient size csv imports are
written to disk at a location defined by
The path set for
MEDIA_ROOT is up to you, but the user that runs the
webserver must have read/write access to the location specified because
it is the webserver than reads and writes the files. In a debian linux,
this is likely to be www-data for a production install. Remember to use
forward slashes for the config file, even for Windows.
MEDIA_ROOT = "/var/openrem/media/"
MEDIA_ROOT = "C:/Users/myusername/Documents/OpenREM/media/"
Generate a new secret key and replace the one in the
local_settings.py file. You can use
http://www.miniwebtool.com/django-secret-key-generator/ for this.
ALLOWED_HOSTS needs to be defined, as the
DEBUG mode is now
False. This needs to contain the server name or IP address that
will be used in the URL in the web browser. For example:
ALLOWED_HOSTS = [ '192.168.56.102', '.doseserver.', 'localhost', ]
A dot before a hostname allows for subdomains (eg www.doseserver), a dot
after a hostname allows for FQDNs (eg doseserver.ad.trust.nhs.uk).
Alternatively, a single
'*' allows any host, but removes the security
the feature gives you.
Customised date format in xlsx exports¶
# TODO: check csv situation The default date form at for OpenREM xlsx exports is dd/mm/yyyy. If you wish to customise this, uncomment the XLSX_DATE line, for example the standard US date format would be:
XLSX_DATE = 'mm/dd/yyyy'
There are two places logfiles need to be configured - here and when starting Celery. The logs defined here capture most of the information; the Celery logs just capture workers starting and tasks starting and finishing.
Configure the filename to determine where the logs are written. In linux, you might want to send them to a sub-folder of
/var/log/. In this example, they are written to the
MEDIA_ROOT; change as appropriate:
import os logfilename = os.path.join(MEDIA_ROOT, "openrem.log") qrfilename = os.path.join(MEDIA_ROOT, "openrem_qr.log") storefilename = os.path.join(MEDIA_ROOT, "openrem_store.log") LOGGING['handlers']['file']['filename'] = logfilename # General logs LOGGING['handlers']['qr_file']['filename'] = qrfilename # Query Retrieve SCU logs LOGGING['handlers']['store_file']['filename'] = storefilename # Store SCP logs LOGGING['handlers']['extractor_file']['filename'] = extractorfilename # Extractor logs
If you want all the logs in one file, simply set them all to the same filename.
In the settings file, there are
verbose log message styles. We recommend you leave these as
LOGGING['handlers']['file']['formatter'] = 'verbose' # General logs LOGGING['handlers']['qr_file']['formatter'] = 'verbose' # Query Retrieve SCU logs LOGGING['handlers']['store_file']['formatter'] = 'verbose' # Store SCP logs LOGGING['handlers']['extractor_file']['formatter'] = 'verbose' # Extractor logs
Next, you can set the logging level. Options are
progressively less logging.
INFO is probably a good choice for most circumstances.
DEBUG is useful if something
is going wrong, but it is quite chatty for routine use!
LOGGING['loggers']['remapp']['level'] = 'INFO' # General logs LOGGING['loggers']['remapp.netdicom.qrscu']['level'] = 'INFO' # Query Retrieve SCU logs LOGGING['loggers']['remapp.netdicom.storescp']['level'] = 'INFO' # Store SCP logs LOGGING['loggers']['remapp.extractors.ct_toshiba']['level'] = 'INFO' # Toshiba RDSR creation extractor logs
Finally, if you are using Linux you can set the system to start a new log file automatically when the current one gets to a certain size. The settings described below don’t work with Windows - we’ll try to include Windows settings in the next release. See issue 483 to find out the progress on this!
To activate the ‘rotating’ log function, uncomment the remaining lines by removing the
# from the beginning of
the lines. For example for the query retrieve logs:
LOGGING['handlers']['qr_file']['class'] = 'logging.handlers.RotatingFileHandler' LOGGING['handlers']['qr_file']['maxBytes'] = 10 * 1024 * 1024 # 10*1024*1024 = 10 MB LOGGING['handlers']['qr_file']['backupCount'] = 5 # number of log files to keep before deleting the oldest one
Configure the local timezone in order to get correct times in the logfiles. The default timezone is set at ‘Europe/London’. Valid options can be found here: http://en.wikipedia.org/wiki/List_of_tz_zones_by_name
TIME_ZONE = 'Europe/London'
Configure the local language. Default language is set at us-english. Valid options can be found here: http://www.i18nguy.com/unicode/language-identifiers.html
LANGUAGE_CODE = 'en-us'
Toshiba CT RDSR creation¶
If you need to import data from older Toshiba CT scanners into OpenREM then the following tools need to be available on the same server as OpenREM:
The paths to these must be set in
local_settings.py for your system:
# Locations of various tools for DICOM RDSR creation from CT images DCMTK_PATH = 'C:/Apps/dcmtk-3.6.0-win32-i386/bin' DCMCONV = os.path.join(DCMTK_PATH, 'dcmconv.exe') DCMMKDIR = os.path.join(DCMTK_PATH, 'dcmmkdir.exe') JAVA_EXE = 'C:/Apps/doseUtility/windows/jre/bin/java.exe' JAVA_OPTIONS = '-Xms256m -Xmx512m -Xss1m -cp' PIXELMED_JAR = 'C:/Apps/doseUtility/pixelmed.jar' PIXELMED_JAR_OPTIONS = '-Djava.awt.headless=true com.pixelmed.doseocr.OCR -'
The example above is for Windows. On linux,
if you have installed the Offis DICOM toolkit with
sudo apt install dcmtk or similar, you can find the path for the
configuration above using the command
which dcmconv. This will be something like
/usr/bin/dcmconv, so the
DCMTK_PATH would be
'/usr/bin and the
DCMCONV would be
os.path.join(DCMTK_PATH, 'dcmconv'). Similarly
JAVA_EXE, which might be
/usr/bin/java. The pixelmed.jar file should be downloaded from
the link above, and you will need to provide the path to where you have saved it.
Create the database¶
In a shell/command window, move into the openrem folder:
- Ubuntu linux:
- Other linux:
Create the database:
python manage.py makemigrations remapp python manage.py migrate python manage.py showmigrations
The last command will list each Django app migrations. Each should have a cross inside a pair of square brackets something like below:
admin [X] 0001_initial auth [X] 0001_initial [X] 0002_alter_permission_name_max_length [X] 0003_alter_user_email_max_length [X] 0004_alter_user_username_opts [X] 0005_alter_user_last_login_null [X] 0006_require_contenttypes_0002 contenttypes [X] 0001_initial [X] 0002_remove_content_type_name remapp [X] 0001_initial sessions [X] 0001_initial sites [X] 0001_initial
Finally, create a Django super user:
python manage.py createsuperuser
Answer each question as it is asked – this user is needed to set up the other users and the permissions.
Add the median database function: PostgreSQL databases only¶
Rename the file
and then run
python manage.py migrate
This command runs the migration file, and will display the text
Applying remapp.0002_0_7_fresh_install_add_median... OK, indicating that the median function has been added.
Start all the services!¶
You are now ready to start the services to allow you to use OpenREM - go to Start all the services to see how!
DICOM Store and query-retrieve¶
The best (and only practical way in a production environment) to get DICOM data into OpenREM is to have a DICOM store node (Store Service Class Provider/SCP) and possibly a query-retrieve service class user too.
To find out more about this, refer to the DICOM Store and QR docs.