include the files .h5 as link and not as path
the files .h5 must be included as link, maybe included also as path (?)
import h5py f = h5py.File("masterFile.h5","w") f["/scan1/measurement/image_01.edf"] = "path/image_01.edf" f["/scan1/measurement/image_02.h5"] = h5py.ExternalLink("path/image_02.h5", "/scan1") f.flush() f.close()
Edited by Roberto Arturo Homs-Regojo