DICOM
Contents
DICOM#
Summary#
A DICOM toolbox.
API#
Anonymisation#
- pymedphys.dicom.anonymise(ds, replace_values=True, keywords_to_leave_unchanged=(), delete_private_tags=True, delete_unknown_tags=None, copy_dataset=True, replacement_strategy=None, identifying_keywords=None)#
A simple tool to anonymise a DICOM dataset.
You can find the list of DICOM keywords that are included in default anonymisation here. These were drawn from DICOM Supp 142
We do not claim conformance to any DICOM Application Level Confidentiality Profile.
- Parameters
ds (
pydicom.dataset.Dataset
) – The DICOM dataset to be anonymised.replace_values (
bool
, optional) – If set toTrue
, DICOM tags will be anonymised using dummy “anonymous” values. This is often required for commercial software to successfully read anonymised DICOM files. If set toFalse
, anonymised tags are simply given empty string values. Defaults toTrue
.keywords_to_leave_unchanged (
sequence
, optional) – A sequence of DICOM keywords (corresponding to tags) to exclude from anonymisation. Private and unknown tags can be supplied. Empty by default.delete_private_tags (
bool
, optional) – A boolean to flag whether or not to remove all private (non-standard) DICOM tags from the DICOM file. These may also contain identifying information. Defaults toTrue
.delete_unknown_tags (
bool
, pseudo-optional) – If left as the default value ofNone
andds
contains tags that are not present in PyMedPhys’ copy ofpydicom
’s DICOM dictionary,anonymise_dataset()
will raise an error. The user must then either passTrue
orFalse
to proceed. If set toTrue
, all unrecognised tags that haven’t been listed inkeywords_to_leave_unchanged
will be deleted. If set toFalse
, these tags are simply ignored. PassFalse
with caution, since unrecognised tags may contain identifying information.copy_dataset (
bool
, optional) – IfTrue
, then a copy ofds
is returned.replacement_strategy (
dict
(keys are VR, value is dispatch function), optional) – If left as the default value ofNone
, the hardcode replacement strategy is used.identifying_keywords (
list
, optional) – If left as None, the default values for/list of identifying keywords are used
- Returns
ds_anon – An anonymised version of the input DICOM dataset.
- Return type
pydicom.dataset.Dataset
Dose#
A suite of functions for manipulating dose in a DICOM context.
- pymedphys.dicom.depth_dose(depths, dose_dataset, plan_dataset)[source]#
Interpolates dose for defined depths within a DICOM dose dataset.
Since the DICOM dose dataset is in CT coordinates the corresponding DICOM plan is also required in order to calculate the conversion between CT coordinate space and depth.
Currently, depth_dose() only supports a dose_dataset for which the patient orientation is HFS and that any beams in plan_dataset have gantry angle equal to 0 (head up). Depth is assumed to be purely in the y axis direction in DICOM coordinates.
- Parameters
depths (numpy.ndarray) – An array of depths to interpolate within the DICOM dose file. 0 is defined as the surface of the phantom using either the
SurfaceEntryPoint
parameter or a combination ofSourceAxisDistance
,SourceToSurfaceDistance
, andIsocentrePosition
.dose_dataset (pydicom.dataset.Dataset) – The RT DICOM dose dataset to be interpolated
plan_dataset (pydicom.dataset.Dataset) – The RT DICOM plan used to extract surface parameters and verify gantry angle 0 beams are used.
- pymedphys.dicom.profile(displacements, depth, direction, dose_dataset, plan_dataset)[source]#
Interpolates dose for cardinal angle horizontal profiles within a DICOM dose dataset.
Since the DICOM dose dataset is in CT coordinates the corresponding DICOM plan is also required in order to calculate the conversion between CT coordinate space and depth and horizontal displacement.
Currently, profile() only supports a dose_dataset for which the patient orientation is HFS and that any beams in plan_dataset have gantry angle equal to 0 (head up). Depth is assumed to be purely in the y axis direction in DICOM coordinates.
- Parameters
displacements (numpy.ndarray) – An array of displacements to interpolate within the DICOM dose file. 0 is defined in the DICOM z or x directions based either upon the
SurfaceEntryPoint
or theIsocenterPosition
depending on what is available within the DICOM plan file.depth (float) – The depth at which to interpolate within the DICOM dose file. 0 is defined as the surface of the phantom using either the
SurfaceEntryPoint
parameter or a combination ofSourceAxisDistance
,SourceToSurfaceDistance
, andIsocentrePosition
.direction (str, one of ('inplane', 'inline', 'crossplane', 'crossline')) –
- Corresponds to the axis upon which to apply the displacements.
’inplane’ or ‘inline’ converts to DICOM z direction
’crossplane’ or ‘crossline’ converts to DICOM x direction
dose_dataset (pydicom.dataset.Dataset) – The RT DICOM dose dataset to be interpolated
plan_dataset (pydicom.dataset.Dataset) – The RT DICOM plan used to extract surface and isocentre parameters and verify gantry angle 0 beams are used.
- pymedphys.dicom.dicom_dose_interpolate(interp_coords, dicom_dose_dataset)[source]#
Interpolates across a DICOM dose dataset.
- Parameters
interp_coords (tuple(z, y, x)) – A tuple of coordinates in DICOM order, z axis first, then y, then x where x, y, and z are DICOM axes.
dose (pydicom.Dataset) – An RT DICOM Dose object