Problem saving oracle large object.

[cartal]

Hi,

I'm trying to save my oracle object using the oracle.to_hdf5 function, but I run into the following error:

---------------------------------------------------------------------------
OverflowError                             Traceback (most recent call last)
<ipython-input-17-b7f5462aee49> in <module>
----> 1 oracle.to_hdf5("/home/large.celloracle.oracle")

~/my-conda-envs/celloracle/lib/python3.6/site-packages/celloracle/trajectory/oracle_core.py in to_hdf5(self, file_path)
     91         dump_hdf5(obj=self, filename=file_path,
     92                   data_compression=compression_opts,  chunks=(2048, 2048),
---> 93                   noarray_compression=compression_opts, pickle_protocol=2)
     94 
     95 

~/my-conda-envs/celloracle/lib/python3.6/site-packages/celloracle/utility/hdf5_processing.py in dump_hdf5(obj, filename, data_compression, chunks, noarray_compression, pickle_protocol)
     92                                          fletcher32=False, shuffle=False)
     93             else:
---> 94                 serialized = _obj2uint(attribute, compression=noarray_compression, protocol=pickle_protocol)
     95                 _file.create_dataset(f"&{k}", data=serialized,
     96                                      chunks=tuple((min(1024, len(serialized)),)),

~/my-conda-envs/celloracle/lib/python3.6/site-packages/celloracle/utility/hdf5_processing.py in _obj2uint(obj, compression, protocol)
     23     An array encoding in bytes (uint8) the object pickled
     24     """
---> 25     zstr = zlib.compress(pickle.dumps(obj, protocol=protocol), compression)
     26     return np.frombuffer(zstr, dtype=np.uint8)
     27 

OverflowError: cannot serialize a string larger than 4GiB

Which seems to be caused by this issue.

Do you have any idea how to fix this?

[KenjiKamimoto-ac]

Hi Carlos, Thank you for using CellOracle!
I updated pickle protocol in the CellOracle now. Could you please uninstall CellOracle and re-install the updated CellOracle, and then please try to save your file again?