def info(self, hdf_path, channel_name=None): """ Print available information about HDF5 file, or specified channel. :param hdf_path: HDF5 file of interest :param channel_name: Print information only concerning specified channel. :return: None """ if not os.path.isfile(hdf_path): sys.exit("File not found!") self.hdf_path = hdf_path lmf = LightMicroscopyHDF(self.hdf_path) if channel_name is not None: print lmf.get_channel(channel_name) else: print lmf lmf.close()
def write_affine(self, hdf_path, channel_name, affine_name, affine_path): """ Reads ITK produced affine file and writes it in nifti and itk compatible formats to a given channel. :param hdf_path: path to the HDF5 file :param channel_name: Identifies the channel to which affine will be written. :param affine_name: Name of the affine, must be unique for channel. :param affine_path: Path to a .txt file containing the affine parameters. :return: None """ self.hdf_path = hdf_path lmf = LightMicroscopyHDF(self.hdf_path) channel = lmf.get_channel(channel_name) channel.write_affine(affine_name, affine_path) lmf.close()