Provides a various set of tools for DICOM header manipulation.

usage: pymedphys dicom [-h]

Positional Arguments

dicom Possible choices: anonymise, merge-contours, adjust-machine-name, adjust-RED, adjust-RED-by-structure-name



Anonymise DICOM files.

pymedphys dicom anonymise [-h] [-o OUTPUT_PATH] [-d] [-f] [-c]
                          [-k [KEYWORD [KEYWORD ...]]] [-p] [-u | -i]

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 overlapping contours within a DICOM structure file

pymedphys dicom merge-contours [-h] [--structures STRUCTURES [STRUCTURES ...]]
                               input_file output_file

Positional Arguments


Named Arguments

--structures The structures for which to run the merge on. If not provided, then all structures will be processed.


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



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

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


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