numpy‑1.14.5+mkl‑cp27‑cp27m‑win_amd64.whl

psycopg2‑2.7.5‑cp27‑cp27m‑win_amd64.whl

Search for and download the following numpy package:

numpy‑1.14.5+mkl‑cp27‑cp27m‑win_amd64.whl

Search for and download the following psycopg2 package:

psycopg2‑2.7.5‑cp27‑cp27m‑win_amd64.whl

https://bitbucket.org/edmcdonagh/pynetdicom/get/default.tar.gz#egg=pynetdicom-0.8.2b2

Double click “Downloads”

Select “Available from local drive…” when option to add Python to PATH appears

Left Click “Windows Powershell”

Pin “Windows Powershell” to taskbar for later use.

cd Downloads
pip install numpy‑1.14.5+mkl‑cp27‑cp27m‑win_amd64.whl
pip install psycopg2‑2.7.5‑cp27‑cp27m‑win_amd64.whl
pip install edmcdonagh-pynetdicom-2da8a57b53b3.tar.gz 

http://erlang.org/download/otp_win64_21.0.1.exe

Accept defaults

https://dl.bintray.com/rabbitmq/all/rabbitmq-server/3.7.7/rabbitmq-server-3.7.7.exe 

Accept defaults

Accept firewall prompts

https://www.enterprisedb.com/downloads/postgres-postgresql-downloads

Select “PostgreSQL 10.4”

Select “Windows x86-64”

Click “Download Now”

Select defaults unless you want an alternate download directory

# Remember the postgres superuser password!

Take tick off Stack Builder launch at the end of the setup

Find postgres 10 -> pgAdmin

Right click to pin pgAdmin to taskbar

Expand Servers

Enter Superuser password

Keep pgadmin opened

Name: openrem

Click Definition

# Remember this password!

Click Privileges

Toggle “Can login?” and “Create Databases?” to “yes”

Click Save

Right click -> Create Database

Database: openrem

Change owner to “openrem”

Click save

https://code.visualstudio.com/download

Select defaults.

Take tick OFF “Register code as default editor…” near end of setup.

# We do this so vscode doesn’t launch python code files instead of python.exe.

Run the following:

pip install openrem==0.8.0

Create folder structure: C:\OpenREM\media

Navigate to “C:\Python27\lib\site-packages\openrem\openremproject”

Rename “local_settings.py.example” to “local_settings.py”

Rename “wsgi.py.example” to “wsgi.py”

Stay in this folder

DATABASES = {
'default': {
'ENGINE': 'django.db.backends.postgresql_psycopg2',
'NAME': 'openrem',
'USER': 'openrem',
'PASSWORD': 'XXXXX',
...
MEDIA_ROOT = 'C:/OpenREM/media'
...
SECRET_KEY = 'XXXXX'
...
XLSX_DATE = 'dd/mm/yyyy'
...
TIME_ZONE = 'Australia/Melbourne'

Save the file

Run the following:

cd C:\Python27\lib\site-packages\openrem
python manage.py  makemigrations remapp
python manage.py migrate
python manage.py createsuperuser

Keep this window open

Navigate to C:\Python27\lib\site-packages\openrem\remapp\migrations

Rename “0002_0_7_fresh_install_add_median.py.inactive” to “0002_0_7_fresh_install_add_median.py”

Run the following:

python manage.py migrate
python manage.py showmigrations

Everything should have a X in it.

python manage.py runserver --insecure 0.0.0.0:80

Browse http://localhost and see if it loads.

Ctrl-C in the powershell window to kill the web server which is required for the next part.

pip install wfastcgi

Start typing (Search) “Turn windows features..”

Select “Turn Windows Features on or off”

Tick “Internet Information Services”

Expand “Internet Information Services” -> “World Wide Web Services:” -> Expand “Application Development Features”

Tick “CGI”

Press OK

Start typing (Search) “IIS”

Pin “Internet Information Services (IIS) Manager) to taskbar

Click “FastCGI Settings” Icon at the top level

Click “Add application”

Change these settings:

Select and click the “…” on the “Environment Variables” line

Add these variable pairs (Case sensitive):

Click OK twice

Right click “C:\OpenREM”  -> Properties -> Security

Click Edit

Click Add

Enter “IIS_IUSRS” and click “OK”

Click the “Allow” checkbox in the modify row for the user “IIS_IUSRS”

Click OK

C:\Python27\lib

C:\Python27\Scripts

Expand Sites

Click on “Default Web Site”

Click on “Basic Settings” in the right action window

Change the Physical Path to “C:\Python27\Lib\site-packages\openrem”

Stay in IIS manager for next step

Click on the “Handler Mappings” Icon

Click on “Add module mapping” in right action window

Change the following settings:

Click OK out of settings window and “Yes” to warning

Navigate to “C:\Python27\Lib\site-packages\openrem”

Create folder called “static”

Navigate to “C:\Python27\Lib\site-packages\openrem\openremproject”

Open “local_settings.py” in editor

Change “STATIC_ROOT” setting to read 'C:/Python27/Lib/site-packages/openrem/static'

Save the file

Expand “Sites”

Right click on “Default Web Site” -> “Add virtual directory”

Settings below:

Click OK

Click the “static” virtual directory

Click “StaticFile” and click “View Ordered List” in the right action window

Click “StaticFile” (again) and “Move Up” in the right action window

Click “Yes” to the warnings

Move “StaticFile” until it is at top of the list

Run the following:

cd C:\Python27\Lib\site-packages\openrem\

python manage.py collectstatic

Type “yes” and hit enter

Site should look the same as when invoked using the inbuilt web server

http://localhost/

OR

Navigate to http://localhost/admin

# This is the admin section for configuring users and changing permissions

Enter a username and password

Scroll down

Click “Save”

On next page Select all “Available groups” and click the right arrow to move them to “Chosen groups”

Scroll down

Click “Save”

# Note there are settings that can be configured for the user at this point but we’ll do it as the user itself

Navigate to base page http://localhost

Login using newly created account (top right)

Check “Plot charts”  and “Submit Query”

Check Patient details in “Store data” if you wish to have these appear.

Click “Submit”

Check “Enable skin dose maps?”

Check OFF “Calculate skin dose map on import” unless you have a lot of CPU processing power

Click Submit

Click View -> Options

Click view tab

Scroll down halfway and uncheck “Hide extensions for known file types”

# This is required for creating files with alternate extensions and needed later.

Create these subfolders:

C:\OpenREM\media\celery
C:\OpenREM\support

https://nssm.cc/release/nssm-2.24.zip

File explorer -> Downloads -> Double click zip file

Navigate to nssm-2.24\win64

Right click nssm -> Copy

Navigate to C:\OpenREM\Support

Paste

# nssm.exe should now be in C:\OpenREM\Support directory

Navigate to C:\OpenREM\Support

Right click empty space -> Left click New -> Text Document

Name the file “celery_service.bat”

Right click and open in editor

Paste the following in. Substitute paths if you’ve deviated from this tutorial:

taskkill /F /IM celery.exe
del /F C:\OpenREM\media\celery\default.pid
C:
cd C:\python27\lib\site-packages\openrem
celery worker -n default -P solo -Ofair -A openremproject -c 4 -Q default --pidfile=C:\OpenREM\media\celery\default.pid --logfile=C:\OpenREM\media\celery\default.log

Save the file

Run the following:

pip install celery==3.1.25

# We install celery 3.1.25 due to issues with 4.X on Windows and supporting modules

Keep window open

C:\OpenREM\support\nssm.exe install "OpenREM Celery Workers"

When window loads change path to:

C:\OpenREM\Support\celery_service.bat

Click install

Run the following command:

net start "OpenREM Celery Workers"

# This is a command line alternative to starting a service via command line instead of Services GUI

Browse to C:\OpenREM\media\celery

Ensure “default.pid” exists.

Check contents of “default.log” and ensure it reads Celery worker started

Create folder C:\Temp

Navigate to C:\Python27\lib\site-packages\openrem\remapp\tests\test_files

Copy all dcm (DICOM) files

Navigate to C:\Temp

Paste files into directory

Run the following

openrem_rdsr.py C:\Temp\RF-RDSR-*.dcm

# This will use the OpenREM RDSR import script to import some Fluoroscopy and Radiography SR modality DICOMs

Login if not already logged in.

Notice the new count of studies

Run the following

openrem_dx.py C:\Temp\DX-Im-*.dcm

# Note this time we used the DX import script to import DX modality files instead of SRs

# Note the additional Radiography cases

Click on Fluoroscopy

Click on the “Siemens AXIOM-Artis” case

Wait for Radiation exposure Incidence Map to be processed

Click “Toggle 2D/3D view”

#  Note the calculated peak skin dose which can be used as estimation. Note that this feature is only supported on specific manufacturers and is experimental.

#  There are many metrics that you can review in your own time but some useful ones include dose area product, dose at reference point,  acquisition protocols, event types, pulse rates.

Click “Plot of mean DAP….”

# Note the various functionality here. After a build up of cases you can use this feature to build Dose Reference Levels, compare different systems and optimise dose.

Click “Export to CSV” in the “Data Export” window

# You can review the contents at a later point. This is to demonstrate functionality.

Select “Orthanc 18.7.1 installer by Osimis…”

Enter rest of details. This can be a personal email address

# The actual installer for the free tool is provided by a corporate partner hence the requirement to provide contact details. One can compile manually but this is a much easier approach.

Download installer from link in email

Double click and install the package keeping default options.

https://bitbucket.org/openrem/openrem/src/012c6cacd2e8dc23695cd912731b444c8314cba6/stuff/openrem_orthanc_config.lua?at=master&fileviewer=file-view-default

Right click “Raw” -> Save link/target as

Save as “openrem_orthanc_config.lua” to C:\OpenREM\Support

OR Save in downloads and move to C:\OpenREM\Support

Change the “LuaScripts” setting to read like this:

"LuaScripts" : [
"C:\\OpenREM\\support\\openrem_orthanc_config.lua"
],

# Scroll down and note your “DicomAet” and “DicomPort” settings. This will be useful later if configuring a PACS system to auto forward. In most cases it will be “ORTHANC” and “4242”

Save the file

Click “Retry as Admin” when prompt appears in bottom left.

Save the file again

Close the file

Create folder C:\OpenREM\Support\dicom

Expand “Services and applications”

Click Services

Find “Orthanc”

Right click -> Restart

Start typing “firewall”

Select “Allow an app through Windows Firewall”

Click “Change settings”

Click “Allow another app…”

Browse to “C:\Program Files\Orthanc Server\Orthanc.exe”

Click “Network Types”

Make sure “Private” is also ticked

Click OK

Click Add

Click OK

Run the following command:

ipconfig

# Note down the “IPv4” Address. We will use this in transmitting files over DICOM send protocol

Download ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/dcmtk363/bin/dcmtk-3.6.3-win64-dynamic.zip

Open Zip file

Copy folder out to C:\ and rename to C:\dcmtk

Run the following

C:\dcmtk\bin\storescu -v 192.168.0.1 4242 C:\Temp\CT-RDSR-*.dcm

# Here we’re sending DICOM files to the DICOM server we just set up. Substitute the IP address for the one you took down earlier. If you are on a virtual machine this may not work if the network is hidden behind a NAT. If you do not know what this means that’s OK, you can do this from the same virtual machine.

OR

Browse to http://192.168.0.1

# Substitute IP address you took down earlier