@ejolly, just tried using the new hdf5 loading for an older file and encoutered this error message:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In[33], line 16
12 f = file_list[0]
14 sub = os.path.basename(f).split('_')[0]
---> 16 fmri_data = Brain_Data(f)
File ~/Github/nltools/nltools/data/brain_data.py:206, in Brain_Data.__init__(self, data, Y, X, mask, **kwargs)
203 else:
204 # Load X and Y dataframes
205 with pd.HDFStore(to_load, "r") as f:
--> 206 self.X = f["X"]
207 self.Y = f["Y"]
209 # Load data and masker stuffs
File ~/opt/anaconda3/lib/python3.11/site-packages/pandas/io/pytables.py:602, in HDFStore.__getitem__(self, key)
601 def __getitem__(self, key: str):
--> 602 return self.get(key)
File ~/opt/anaconda3/lib/python3.11/site-packages/pandas/io/pytables.py:813, in HDFStore.get(self, key)
811 if group is None:
812 raise KeyError(f"No object named {key} in the file")
--> 813 return self._read_group(group)
File ~/opt/anaconda3/lib/python3.11/site-packages/pandas/io/pytables.py:1878, in HDFStore._read_group(self, group)
1877 def _read_group(self, group: Node):
-> 1878 s = self._create_storer(group)
1879 s.infer_axes()
1880 return s.read()
File ~/opt/anaconda3/lib/python3.11/site-packages/pandas/io/pytables.py:1752, in HDFStore._create_storer(self, group, format, value, encoding, errors)
1750 tt = "generic_table"
1751 else:
-> 1752 raise TypeError(
1753 "cannot create a storer if the object is not existing "
1754 "nor a value are passed"
1755 )
1756 else:
1757 if isinstance(value, Series):
TypeError: cannot create a storer if the object is not existing nor a value are passed
I don't believe there should be any metadata stored in these files. Is this something is simple as just checking and initializing with an empty value?
@ejolly , I know @nirjacoby has also encountered this issue. Let us know if there is anything we can do to help fix it. It might make sense for you to take the lead on this one.
@ejolly, just tried using the new hdf5 loading for an older file and encoutered this error message:
I don't believe there should be any metadata stored in these files. Is this something is simple as just checking and initializing with an empty value?