Upgrade to OpenREM 0.8.0

Headline changes

  • This release has extensive automated testing for large parts of the codebase (for the first time)
  • Code quality is much improved, reduced duplication, better documentation, many bugs fixed
  • Imports: RDSR from a wider range of systems now import properly
  • Imports: Better distinction and control over defining RDSR studies as RF or DX
  • Imports: Code and instructions to generate and import RDSR from older Toshiba CT scanners
  • Imports: DICOM Query-Retrieve functionality has been overhauled
  • Imports, display and export: Better handling of non-ASCII characters
  • Interface: More detailed, consistent and faster rendering of the data in the web interface
  • Interface: Maps of fluoroscopy radiation exposure incident on a phantom (Siemens RDSRs only)
  • Interface: More and better charts, including scatter plots for mammography
  • Exports: Much faster, and more consistent

Upgrading an OpenREM server with no internet access

Follow the instructions found at Upgrade an offline OpenREM installation, before returning here to update the database and configuration.

Upgrading from version 0.7.4

Upgrade

  • Back up your database

    • For PostgreSQL you can refer to Backup the database
    • For a non-production SQLite3 database, simply make a copy of the database file
  • Stop any Celery workers

  • If you are using a virtualenv, activate it

  • Install the new version of OpenREM:

pip install openrem==0.8.0b1

Migrate the database

In a shell/command window, move into the openrem folder:

  • Ubuntu linux: /usr/local/lib/python2.7/dist-packages/openrem/
  • Other linux: /usr/lib/python2.7/site-packages/openrem/
  • Linux virtualenv: lib/python2.7/site-packages/openrem/
  • Windows: C:\Python27\Lib\site-packages\openrem\
  • Windows virtualenv: Lib\site-packages\openrem\
python manage.py makemigrations remapp
python manage.py migrate remapp

Update the configuration

  • Set the date format for xlsx exports (need to check csv situation). Copy the following code into your local_settings.py file if you want to change it from dd/mm/yyy:
# Date format for exporting data to Excel xlsx files.
# Default in OpenREM is dd/mm/yyyy. Override it by uncommenting and customising below; a full list of codes is available
# at https://msdn.microsoft.com/en-us/library/ee634398.aspx.
# XLSX_DATE = 'mm/dd/yyyy'
  • Consider setting the timezone and language in local_settings.py. See local_settings.py.example.
  • Add the new extractor log file configuration to the local_settings.py - you can copy the ‘Logging configuration’ section from local_settings.py.example if you haven’t made many changes to this section. See the Log file settings in the install instructions.

Adding legacy Toshiba CT functionality

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 for DCMMKDIR and 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.

Restart all the services

Follow the guide at Start all the services.