def DataCopyWithOverlay(self, dcmfilelist, out_dir, overlays):
        """
        Function make 3D data from dicom file slices

        :dcmfilelist list of sorted .dcm files
        :overlays dictionary of binary overlays. {1:np.array([...]), 3:...}
        :out_dir output directory

        """
        dcmlist = dcmfilelist
        # data3d = []

        for i in range(len(dcmlist)):
            onefile = dcmlist[i]

            logger.info(onefile)
            data = dicom.read_file(onefile)

            for i_overlay in overlays.keys():
                overlay3d = overlays[i_overlay]
                data = self.encode_overlay_slice(data,
                                                 overlay3d[-1 - i, :, :],
                                                 i_overlay)

            # construct output path
            head, tail = os.path.split(os.path.normpath(onefile))
            filename_out = os.path.join(out_dir, tail)

# save
            data.save_as(filename_out)
def DataCopyWithOverlay ( self , dcmfilelist , out_dir , overlays ) : dcmlist = dcmfilelist for i in range ( len ( dcmlist ) ) : onefile = dcmlist [ i ] logger . info ( onefile ) data = dicom . read_file ( onefile ) for i_overlay in overlays . keys ( ) : overlay3d = overlays [ i_overlay ] data = self . encode_overlay_slice ( data , overlay3d [ - 1 - i , : , : ] , i_overlay ) head , tail = os . path . split ( os . path . normpath ( onefile ) ) filename_out = os . path . join ( out_dir , tail ) data . save_as ( filename_out )
Function make 3D data from dicom file slices

        :dcmfilelist list of sorted .dcm files
        :overlays dictionary of binary overlays. {1:np.array([...]), 3:...}
        :out_dir output directory