DICOM Files¶

Positional Arguments
Sub-commands:

Provides a various set of tools for DICOM header manipulation.

usage: pymedphys dicom [-h]
                       {anonymise,adjust-machine-name,adjust-RED,adjust-RED-by-structure-name}
                       ...

Positional Arguments ¶

dicom

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

Sub-commands:¶

anonymise ¶

Anonymise DICOM files.

pymedphys dicom anonymise [-h] [-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 ¶

`-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

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