DICOM Files
Contents
DICOM Files#
Provides a various set of tools for DICOM header manipulation.
usage: pymedphys dicom [-h]
{anonymise,merge-contours,adjust-machine-name,adjust-RED,adjust-RED-by-structure-name,listen,send}
...
Positional Arguments#
- dicom
Possible choices: anonymise, merge-contours, adjust-machine-name, adjust-RED, adjust-RED-by-structure-name, listen, send
Sub-commands#
anonymise#
Anonymise DICOM files.
pymedphys dicom anonymise [-h] [-o OUTPUT_PATH] [-d] [-f] [-c]
[-k [KEYWORD [KEYWORD ...]]] [-p] [-u | -i]
input_path
Positional Arguments#
- input_path
Input file or directory path. If a directory is supplied, all DICOM files within the directory and its subdirectories will be anonymised
Named Arguments#
- -o, --output_path
Output file or directory path.
- -d, --delete_original_files
Use this flag to delete the original, non-anonymised files in the processed directory. Each original file will only be deleted if anonymisation completed successfully for that file.
Default: False
- -f, --preserve_filenames
Use this flag to preserve the original filenames in the anonymised DICOM filenames. Note that ‘_Anonymised.dcm’ will still be appended. Use with caution, since DICOM filenames may contain identifying information
Default: False
- -c, --clear_values
Use this flag to simply clear the values of all of the identifying elements in the anonymised DICOM files, as opposed to replacing them with ‘dummy’ values.
Default: False
- -k, --keywords_to_leave_unchanged
A space-separated list of DICOM keywords (e.g. ‘PatientName’) to exclude from anonymisation and error checking.
- -p, --keep_private_tags
Use this flag to preserve private tags in the anonymised DICOM files.
Default: False
- -u, --delete_unknown_tags
Use this flag to delete any unrecognised tags from the anonymised DICOM files.
Default: False
- -i, --ignore_unknown_tags
Use this flag to ignore any unrecognised tags in the anonymised DICOM files.
Default: False
merge-contours#
Merge overlapping contours within a DICOM structure file
pymedphys dicom merge-contours [-h] [--structures STRUCTURES [STRUCTURES ...]]
input_file output_file
Positional Arguments#
- input_file
- output_file
Named Arguments#
- --structures
The structures for which to run the merge on. If not provided, then all structures will be processed.
adjust-machine-name#
Change the machine name in an RT plan DICOM file
pymedphys dicom adjust-machine-name [-h]
input_file output_file new_machine_name
Positional Arguments#
- input_file
- output_file
- new_machine_name
adjust-RED#
Adjust the RED of structures within an RT structure DICOM file
pymedphys dicom adjust-RED [-h] [-i]
input_file output_file adjustment_map
[adjustment_map ...]
Positional Arguments#
- input_file
- output_file
- adjustment_map
An alternating list of structure name and then its associated RED. For example,
pymedphys dicom adjust-RED
input.dcm output.dcm
struct_name 1.5 another_struct_name 0.2
Named Arguments#
- -i, --ignore_missing_structure
Use this flag to no longer raise an error when a defined structure name doesn’t exist within the input DICOM file.
Default: False
adjust-RED-by-structure-name#
Use structure naming conventions to automatically adjust the relative electron density of a structure within a DICOM RT Structure set. For example, naming a structure a_structure_name RED=1.15
will cause that structure to have an override of 1.15 applied.
pymedphys dicom adjust-RED-by-structure-name [-h] input_file output_file
Positional Arguments#
- input_file
input_file
- output_file
output_file
listen#
Start a DICOM listener on the specified port
pymedphys dicom listen [-h] [--host HOST] [-d STORAGE_DIRECTORY] [-a AETITLE]
port
Positional Arguments#
- port
The port on which to listen
Named Arguments#
- --host
The host/IP to bind to
Default: “0.0.0.0”
- -d, --storage_directory
Default: “.”
- -a, --aetitle
The AE Title of this listen service
Default: “PYMEDPHYS”
send#
Send DICOM objects to a DICOM endpoint
pymedphys dicom send [-h] [-a AETITLE] host port [dcmfiles [dcmfiles ...]]
Positional Arguments#
- host
The host name/IP of the DICOM listener
- port
The port of the DICOM listener
- dcmfiles
Path to DICOM objects to send
Named Arguments#
- -a, --aetitle
The Called AE Title
Default: “PYMEDPHYS”