PyMAIA.utils.volume_utils module#

PyMAIA.utils.volume_utils.convert_DICOM_folder_to_NIFTI_image(patient_dicom_folder, patient_nifti_folder)[source]#

Converts a given Patient DICOM folder into NIFTI format, saving the DICOM Studies in different folders.

Parameters:

  • patient_dicom_folder (Union[str, PathLike]) – DICOM folder containing a single patient Studies.

  • patient_nifti_folder (Union[str, PathLike]) – Output NIFTI folder used as stem to save the DICOM Studies. The Study index is appended to this path to create the corresponding NIFTI study folder path.

Return type:

Dict[str, str]

Returns:

Dictionary mapping each Patient -> Study ID to the corresponding StudyInstanceUID

PyMAIA.utils.volume_utils.dcm2nii_CT(CT_dcm_path, nii_out_path)[source]#

Conversion of CT DICOM to nifti and save in nii_out_path.

Parameters:

  • CT_dcm_path (Union[str, PathLike]) – CT DICOM folder path.

  • nii_out_path (Union[str, PathLike]) – Output NIFTI file path.

PyMAIA.utils.volume_utils.dcm2nii_mask(mask_dcm_path, nii_out_path, ref_nii_path)[source]#

Converts a SEG DICOM volume into NIFTI format. Requires an existing NIFTI file to derive the corresponding affine transform.

Parameters:

  • mask_dcm_path (Union[str, PathLike]) – SEG DICOM folder.

  • nii_out_path (Union[str, PathLike]) – NIFTI file saved as output.

  • ref_nii_path (Union[str, PathLike]) – Reference NIFTI used to correctly saved the segmentation volume.

PyMAIA.utils.volume_utils.dcm2nii_seg(mask_dcm_path, nii_out_path, ref_nii_path)[source]#

Conversion of SEG DICOM to NIFTI, using a reference NIFTI image.

Parameters:

  • mask_dcm_path (Union[str, PathLike]) – SEG DICOM folder.

  • nii_out_path (Union[str, PathLike]) – NIFTI file saved as output.

  • ref_nii_path (str) – Reference NIFTI used to correctly saved the segmentation volume.

PyMAIA.utils.volume_utils.normalize_PET_to_SUV_BW(dicom_pet_series_folder, suv_pet_filename)[source]#

SUV BW Normalization of DICOM PET volume. The resulting normalized PET volume is saved at suv_pet_filename.

Parameters:

  • dicom_pet_series_folder (Union[str, PathLike]) – DICOM PET Folder to be normalized.

  • suv_pet_filename (Union[str, PathLike]) – Normalized SUV PET file location.

PyMAIA.utils.volume_utils.resample_image(nii_input_path, nii_ref_path, nii_out_path)[source]#

Resample Input NIFTI to match Reference NIFTI size and spacing.

Parameters:

  • nii_input_path (Union[str, PathLike]) – Input NIFTI File Path.

  • nii_ref_path (Union[str, PathLike]) – Reference NIFTI File Path.

  • nii_out_path (Union[str, PathLike]) – Resampled Output NIFTI File Path.