Importing data to OpenREM¶
Importing dose related data from DICOM files¶
If you are using linux, or for Windows if you have put C:\Python27\;C:\Python27\Lib\site-packages;C:\Python27\Scripts onto your system path, you should be able to import from the command line:
Radiation Dose Structured Reports¶
In linux, or using an advanced shell in Windows, you can use wildcards to process a number of files at once, ie:
This feature will be added for Windows users with the standard cmd.exe shell in a future version, and is tracked as issue #9
For mammography DICOM images¶
The facility for extracting dose information from mammography DICOM images has been designed and tested with images created with the GE Senographe DS. It has now been tested in a limited fashion with the images generated by the following systems:
- GE Senographe Essential
- Hologic Selenia
- Siemens Inspiration
See Mammography module for testing restrictions.
For radiographic DICOM images¶
It is now possible with OpenREM version 0.5.0 to import dose information from DX and CR images from digital radiography units. As yet, it hasn’t been tested extensively.
For CT dose summary files from Philips CT scanners¶
Importing dose related data from csv files using the command line¶
Patient height and weight information¶
If height and weight data is not available in the DICOM data, but is available from another source, then it can be imported into the database using the openrem_ptsizecsv.py function. Normally the key to match the size information with the studies in the database will be the accession number; however in some situations this isn’t available and the Study Instance UID can be used instead.
openrem_ptsizecsv.py [-h] [-u] [-v] csvfile id height weight
- -h, --help
- Print the help text.
- -u, --si-uid
- Use Study Instance UID instead of Accession Number.
- -v, --verbose
- New in 0.3.7 Print to the standard output the success or otherwise of inserting each value.
- csv file containing the height and/or weight information and study identifier. Other columns will be ignored. Use quotes if the filepath has spaces.
- Column title for the accession number or study instance UID. Use quotes if the title has spaces.
- Column title for the patient height (DICOM size) - if this information is missing simply add a blank column with a suitable title. Use quotes if the title has spaces.
- Column title for the patient weight - if this information is missing simply add a blank column with a suitable title. Use quotes if the title has spaces.
Changed in version 0.3.7: Verbosity flag added to supress printing to the standard output unless requested.