DICOM Conversion#

NIfTI to DICOM RTSTUCT#

platipy.dicom.io.nifti_to_rtstruct.convert_nifti(dcm_path, mask_input, output_file, color_map=<matplotlib.colors.LinearSegmentedColormap object>)#

Convert a set of masks to a DICOM RTStruct object.

This function now utilises the rt-utils package: https://github.com/qurit/rt-utils We keep this function in here for compatibility

Parameters:

  • dcm_path (str|pathlib.Path) – Path to the reference DICOM series

  • mask_input (dict|list) – A dictionary containing the name as key and image as value. Or a list of string with comma separated name and mask paths (name,path)

  • output_file (str|pathlib.Path) – The path to the file to write the RTStruct

  • color_map (matplotlib.colors.Colormap, optional) – Colormap to use for output. Defaults to matplotlib.colormaps.get_cmap(“rainbow”).

DICOM RTSTRUCT to NIfTI#

platipy.dicom.io.rtstruct_to_nifti.convert_rtstruct(dcm_img, dcm_rt_file, prefix='Struct_', output_dir='.', output_img=None, spacing=None, replace_slashes_with='')#

Convert a DICOM RTSTRUCT to NIFTI masks.

The masks are stored as NIFTI files in the output directory

Parameters:

  • dcm_img (str|pathlib.Path) – Path to the reference DICOM image series

  • dcm_rt_file (str|pathlib.Path) – Path to the DICOM RTSTRUCT file

  • prefix (str, optional) – The prefix to give the output files. Defaults to “Struct_”.

  • output_dir (str|pathlib.Path, optional) – Path to the output directory. Defaults to “.”.

  • output_img (str|pathlib.Path, optional) – If set, write the reference image to this file as in NIFTI format. Defaults to None.

  • spacing (list, optional) – Values of image spacing to override. Defaults to None.

  • replace_slashes_with (str, optional) – String to replace “/” and “” with. Set to None disable replacement of slashes. Defaults to “”.

platipy.dicom.io.rtstruct_to_nifti.fix_missing_data(contour_data)#

Fixed a set of contour data if there are values missing

Parameters:

contour_data (pydicom.Sequence) – The contour sequence from the DICOM object

Returns:

The array of contour data with missing values fixed

Return type:

np.array

platipy.dicom.io.rtstruct_to_nifti.read_dicom_image(dicom_path)#

Read a DICOM image series

Parameters:

dicom_path (str|pathlib.Path) – Path to the DICOM series to read

Returns:

The image as a SimpleITK Image

Return type:

sitk.Image

platipy.dicom.io.rtstruct_to_nifti.read_dicom_struct_file(filename)#

Read a DICOM RTSTRUCT file

Parameters:

filename (str|pathlib.Path) – Path to the RTSTRUCT to read

Returns:

The RTSTRUCT as a DICOM Dataset

Return type:

pydicom.Dataset

platipy.dicom.io.rtstruct_to_nifti.transform_point_set_from_dicom_struct(dicom_image, dicom_struct, spacing_override=None)#

Converts a set of points from a DICOM RTSTRUCT into a mask array

Parameters:

  • dicom_image (sitk.Image) – The reference image

  • dicom_struct (pydicom.Dataset) – The DICOM RTSTRUCT

  • spacing_override (list) – The spacing to override. Defaults to None

Returns:

Returns a list of masks and a list of structure names

Return type:

tuple

DICOM RTDOSE to NIfTI#

platipy.dicom.io.rtdose_to_nifti.convert_rtdose(dcm_dose, force=False, dose_output_path=None)#

Convert DICOM RTDose to SimpleITK image, saving as NiFTI if needed.

Parameters:

  • dcm_dose (str|path) – Path to DICOM dose file

  • force (bool) – force flag to pass to pydicom

  • dose_output_path (str|path, optional) – If set, NiFTI file will be written. Defaults to None.

Returns:

The dose grid as a SimpleITK image

Return type:

SimpleITK.Image